Protein/solubility folding assessed by structural complementation

ABSTRACT

Many proteins, when produced recombinantly, suffer from improper processing, folding and lack normal solubility. Modified proteins, including those indicative of disease states, also can have such defects. The present invention is directed to methods of identifying proper and improper protein folding, aberrant processing and/or insolubility. The method relies on the use of two components: a specialized fusion protein and structural complementation. The fusion protein contains sequences from the protein of interest and one portion of a marker protein that, by itself, is not active. A host cell then provides the remainder of the marker protein that serves to “complement” the function of the fused marker protein such that their association restores activity, permitting detection.

The U.S. Government may own rights in the application pursuant tofinding from the National Institutes of Health (DK49835).

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to the fields of biochemistry, cellularbiology and molecular biology. More particularly, it relates to thefield of protein biochemistry, and specifically, to the use of an assayfor determining protein folding and solubility.

2. Description of Related Art

There are a wide variety of potential applications for a genetic systemenabling rapid and efficient evaluation of protein solubilitycharacteristics in vivo. One of the cornerstones of biotechnology is theability to express target proteins in functional form in vivo ingenetically-engineered organisms. However, many important targetproteins are not efficiently expressed in soluble form in bacteria suchas E. coli, due at least in part to the complexity of the proteinfolding process in vivo (Houry et al., 1999). When encountering a targetprotein that fails to be expressed in soluble form in vivo, the yield ofsoluble protein can often be improved by optimizing various factors suchas the primary sequence of the target protein (Huang et al., 1996) orthe genetic background or growth conditions of the bacterium (Hung etal., 1998; Brown et al., 1997; Blackwell & Horgan, 1991; Bourot et al.,2000; Sugihara & Baldwin, 1988; Wynn et al., 1992). However, existingassays for protein expression in soluble form are tedious, usuallyrequiring lysis and fractionation of cells followed by protein analysisby SDS-polyacrylamide gel electrophoresis. Using this traditionalapproach, screening for protein constructs and/or physiologicalconditions yielding improved solubility is inefficient, and geneticselection is impossible.

Protein folding diseases represent a second area in which proteinsolubility characteristics are of vital medical and technologicalimportance (Thomas et al., 1995; Dobson, 1999). These diseases, whichhave proven particularly refractory to pharmaceutical development, arecaused either by misfolding of a protein during biosynthesis subsequentto acquiring some mutation (Brown et al., 1997; Thomas et al., 1992; Raoet al., 1994) or by aberrant protein processing leading to the formationof an aggregation-prone product, such as the peptide forming the amyloidplaques associated with Alzheimer's disease (Tan & Pepys, 1994; Harper &Lansbury, 1997), SOD1 in amyotropic lateral sclerosis (Bruijn et al.,1998), α-synuclein in Parkinson's disease (Galvin et al., 1983), amyloidA and P deposits in systemic amyloidosis (Hind et al., 1983),transthyretin fibrils in fatal familial insomnia (Colon & Kelly, 1992)and the intranuclear inclusions associated with polyglutamine expansionswhich cause Huntington's disease (Martin & Gusella, 1986; HDCRG, 1993;Davies et al., 1997), spinocerebellar ataxia (Wells & Warren, 1998),spinobulbar muscular atrophy (La Spada et al., 1991), and Machado-JosephDisease (Kawaguchi et al., 1994). The ability to rapidly and efficientlyscreen for protein solubility in vivo could also be applied to thedevelopment of assays for pharmaceutical compounds preventing themisfolding or aggregation of proteins involved in protein foldingdiseases (i.e., assays for compounds that prevent precipitation of suchaggregation-prone proteins).

Thus, there remains a need in the field for improved methods ofscreening for protein folding and solubility.

SUMMARY OF THE INVENTION

The present invention involves the use of a genetic system based onstructural complementation (Richards & Vithayati, 1959; Ullmann et al.,1967; Taniuichi & Anfinsen, 1971; Zabin & Villarejo, 1975; Pecorari etal., 1993; Schonberger et al., 1996) of a selectable marker protein canbe used as the basis of a direct in vivo solubility assay. Structuralcomplementation involves the division of a protein into two componentsegments which must be combined to form a stable and fully functionalstructure. The specific implementation of the method is an adaptation ofthe classic α-complementation system of β-galactosidase (β-gal) (Ullmannet al., 1967). However, the same concept could potentially be applied toother selectable genetic markers like chloramphenicol transacetylase oreven screenable markers like the green fluorescent protein (althoughappropriately complementing fragments of these proteins would have to bedeveloped first). β-gal can be divided into two fragments (α and ω)capable of associating with each other to form an active enzyme (Ullmannet al., 1967). Redistribution of the α-fragment from the soluble to theinsoluble fraction in E. coli cells leads to a reduction in the level ofβ-gal activity which can be assayed either during growth on indicatoragar plates using the chromogenic substrate X-gal, or in suspensionculture. Fusion of the α-fragment to the C-terminus of a target proteinleads to the formation of a chimeric protein with solubility propertiessimilar to that of the target protein alone. Thus, β-gal activity levelsreport the solubility of the target fusion. By contrast, three extantsystems for monitoring solubility and misfolding in vivo rely on the useof fusions with the full-length maker proteins β-gal (Lee et al., 1990),GFP (Waldo et al., 1999) and CAT (Maxwell et al., 1999). It is welldocumented that the solubility properties of protein fusions to intactmarker enzymes tend to be dominated by the solubility properties of themarker enzyme, as evidenced by the use of MBP (Ko et al., 1993; Kapustet al., 1999), thioredoxin (Papouchado et al., 1997), and GST (Wang etal., 1999) fusions to enhance the solubility of some otherwise insolubleprotein constructs. Such a colorimetric plate assay should be readilyadapted to efficient high-throughput screening.

Thus, there is provided, a method for assessing protein folding and/orsolubility comprising (a) providing an expression construct comprising(i) a gene encoding fusion protein, said fusion protein comprising aprotein of interest fused to a first segment of a marker protein,wherein said first segment does not affect the folding or solubility ofthe protein of interest, and (ii) a promoter active in said host celland operably linked to said gene, (b) expressing said fusion protein ina host cell that also expresses a second segment of said marker protein,wherein said second segment is capable of structural complementationwith said first segment, and (c) determining structural complementation,wherein a greater degree of structural complementation, as compared tostructural complementation observed with appropriate negative controls,indicates proper folding and/or solubility of said protein.

The fusion may be N- or C-terminal to said protein of interest. Themarker protein may be selected from the group consisting of a targetbinding protein, an enzyme, a protein inhibitor, and a chromophore.Examples include ubiquitin, green fluorescent protein, blue fluorescentprotein, yellow fluorescent protein, luciferase, aquorin,β-galactosidase, cytochrome c, chymotrypsin inhibitor, RNase,phosphoglycerate kinase, invertase, staphylococcal nuclease, thioredoxinC, lactose permease, amino acyl tRNA synthase, and dihydrofolatereductase. In the particular case of β-galactosidase, the first segmentis the α-peptide of β-galactosidase, and said second segment is theω-peptide of β-galactosidase. In certain embodiments the marker proteinis associated with a detectable phenotype, including enzymatic activity,chromophore or fluorophore activity.

The protein of interest may be Alzheimer's amyloid peptide (Aβ), SOD1,presenillin 1 and 2, α-synuclein, amyloid A, amyloid P, CFTR,transthyretin, amylin, lysozyme, gelsolin, p53, rhodopsin, insulin,insulin receptor, fibrillin, α-ketoacid dehydrogenase, collagen,keratin, PRNP, immunoglobulin light chain, atrial natriuretic peptide,seminal vesicle exocrine protein, β2-microglobulin, PrP, precalcitonin,ataxin 1, ataxin 2, ataxin 3, ataxin 6, ataxin 7, huntingtin, androgenreceptor, CREB-binding protein, dentaorubral pallidoluysianatrophy-associated protein, maltose-binding protein, ABC transporter,glutathione S transferase, and thioredoxin.

The gene encoding the second segment may be carried on a chromosome ofsaid host cell or episomally. The host cell may be a bacterial cell, aninsect cell, a yeast cell, a nematode cell, and a mammalian cell.Examples include E. coli., C. elegans, or S. fugeria, and a variety ofmammalian cells. Preferred promoters include Taq promoter; T7 promoter,or P_(lac) promoter (bacterial), CupADH, Gal (yeast) or PepCk or tk(mammalian).

In particular embodiment, the method utilizes a negative control that isa host cell lacking the second segment of said marker protein and/or afusion protein that is improperly folded and/or insoluble.

In another embodiment, there is provided, a method for screening proteinfolding and/or solubility mutants comprising (a) providing a geneencoding fusion protein comprising (i) a protein of interest and (ii) afirst segment of a marker protein, wherein said first segment does notaffect the folding or solubility of the protein of interest, whereinsaid fusion protein is not properly folded and/or soluble when expressedin said host cell, and (ii) a promoter active in said host cell andoperably linked to said gene, wherein said fusion protein is notproperly folded and/or soluble when expressed in said host cell, (b)mutagenizing that portion of the gene encoding said protein of interest,(c) expressing said fusion protein in a host cell that expresses asecond segment of said marker protein, wherein said second segment iscapable of structural complementation with said first segment, and (d)determining structural complementation, wherein a relative increase instructural complementation, as compared to the structuralcomplementation observed with the unmutagenized fusion protein,indicates an increase in proper folding and/or solubility of saidprotein.

In yet another embodiment, there is provided a method for screeningcandidate modulator substance that modulates protein folding and/orsolubility comprising (a) providing an expression construct comprising(i) a gene encoding fusion protein, said fusion protein comprising aprotein of interest fused to a first segment of a marker protein,wherein said first segment does not affect the folding or solubility ofthe protein of interest, and (ii) a promoter active in said host celland operably linked to said gene, (b) expressing said fusion protein ina host cell that expresses a second segment of said marker protein,wherein said second segment is capable of structural complementationwith said first segment, (c) contacting the host cell with saidcandidate modulator substance; and (d) determining structuralcomplementation, wherein a relative change in structuralcomplementation, as compared to the structural complementation observedin the absence of said candidate modulator substance, indicates thatsaid candidate modulator substance is a modulator of protein foldingand/or solubility. The candidate modulator substance may be a protein, anucleic acid or a small molecule.

Following long-standing patent language convention, the terms “a” or“an,” when used in conjunction with “comprising,” may mean one or morethan one, herein the description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIGS. 1A and 1B: An in vivo solubility assay based on structuralcomplementation. (FIG. 1A) A schematic depicting the complementationsolubility assay. P (squares) represents the target protein, and α(triangles) and ω (trapezoids) represent each of the complementingfragments of the tetrameric β-galactosidase. Brackets indicate theconcentration dependence of the assay regarding the availability ofsoluble (folded) target/a fusion. K_(d) is indicated solely to highlightthe concentration-dependent equilibrium association/dissociationreaction. (FIG. 1B) A schematic representation of the targetprotein/α-fragment C-terminal fusion expression construct (α-fragment,residues 7-58 from full length β-galactosidase). “HA” indicates theposition of the inserted influenza hemagglutinin (HA) immuno-tag(residue sequence YPYDVPDYA) present in some of the constructs examined.

FIG. 2. Correlation of β-galactosidase activity with fusion proteinsolubility and folding. A scatter plot correlating the in vitroβ-galactosidase activity measured in cell lysates (see Table 1) with thefraction soluble (open circles) and the reported periplasmic yield(filed squares) for each of the MBP/α-fragment fusion proteins examined.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Protein misfolding is the basis of a number of human diseases. It alsopresents a sizable obstacle to the production of functional recombinantproteins. In addition, there is a tremendous potential to modulate invivo function of proteins by modulating protein folding. To date, thestudy of misfolding and its circumvention has required development ofspecific assays for each individual case.

However, for maximum utility, such a method should provide an easilymeasured signal, be sensitive to subtle changes in the solubility of thetarget protein over a wide concentration range, allow phenotypicselection of the soluble protein, and have minimal effect on thesolubility of the target protein. The present invention offers each ofthese advantages.

The present invention utilizes generalized fusion constructs and thephenomenon of “structural complementation” to examine protein foldingand/or solubility in cell- or organism-based screening. In a particularembodiment, the α and ωpeptides of β-galactosidase are used, the firstas a fusion partner for a given protein of interest, in acomplementation assay. Where the protein of interest is properly folded,the fusion remains soluble and can associate the other peptide ofβ-galactosidase, permitting enzyme activity and detection. A variety ofdifferent host cells, “structural complementation” pairs (enzymes,binding proteins, chromophores) and target proteins can be used.

The studies presented herein demonstrate that this system reliablyreports on the solubility of eight fused target proteins: the maltosebinding protein and mutants thereof, the first nucleotide bindingdomains of the cystic fibrosis transmembrane conductance regulator andthe branched chain amino acid transporter from the hyperthermophilicarcheon methanococcus jannaschii, and the Aβ peptide of the Alzheimer'sprecursor protein. The fact that the signal produced by the fusions isproportional to the solubility of the nucleotide binding domain targetswhen expressed without the α-fragment indicates that this relativelysmall polypeptide does not significantly effect the solubility of thetarget protein, unlike fusions to a larger marker protein (e.g., M13P,Harper and Lansbury, 1997). This could provide a significant advantageover two recently reported solubility monitoring systems that rely onfusions with larger soluble proteins, namely full length β-gal (Lee etal., 1990), GFP (Waldo et al., 1999) and CAT (Maxwell et al., 1999). Itis well-documented that fusions with highly soluble proteins such as GST(Wang et al., 1999), MBP (Ko et al., 1993), and thioredoxin (Papouchadoet al., 1997), and the immunoglobulin binding domain (GB1) (Huth et al.,1997) significantly improve the solubility properties of a variety ofexpressed proteins. Thus, it is reasonable to expect that in some cases,GFP and CAT may have a significant effect on the solubility of thetarget.

As mentioned above, this system has several potential uses. For example,recombinant production systems can be tested to determine if thepolypeptide to be produced is properly folded. In addition, targetproteins may be diagnostic of disease states. The system also could findutility in the development and selection of bacterial strainsparticularly effective at expressing and folding heterologous proteins,or for phenotypic selection of a wide variety of proteins in their studyby random mutagenesis. These powerful approaches currently are limitedto proteins which themselves are required for a measurable cellularfunction. Thus, the present solubility detection system provides animportant avenue for understanding fundamental biological processes suchas how primary sequence directs the formation of a uniquethree-dimensional structure, or the identity and mechanisms of cellularsystems important for efficient protein maturation.

One aspect of the invention is the minimal impact of the fusion partnerson the protein of interest. The presence of only “systematic” effects(i.e., similar both in the presence and absence of either drug ormutation) on the solubility of the target permits ready comparison. Thisactually provides the added advantage of beign able to adjust thesensitivity of the assay depending on the target protein of interest.Recent discovery of mutations in the α subunit permit “tuning” of theα-θ interaction which also can be used for altering the sensitivity.

Perhaps the most exciting application of the system is the discovery ofdrugs which modulate the folding of disease related proteins.Previously, the search for pharmaceuticals has focused on theidentification of compounds which inhibit cellular processes. However,the increasing prevalence of diseases associated with protein misfoldingsuch as Huntington's disease, Alzheimer's disease, Parkinson's disease,cystic fibrosis, amyotropic lateral schlerosis, Creutzfeld-Jacobdisease, and some forms of diabetes and cancer presents a new challengefor the pharmaceutical industry. The identification of drugs whichtarget proteins with a propensity to misfold requires the development ofnovel screening and assay methodologies such as the α-complementationsystem described herein. Encouraging evidence that such pharmaceuticalsmay be identified has recently been provided by Rastinejad andco-workers (Foster et al., 1999) who reported the identification of aclass of compounds which stabilized a folding mutant of p53 in a solubleand functional conformation, thereby rescuing its ability to preventtumor growth in mice.

Various aspects of the invention are described, in greater detail, inthe following pages.

A. Protein Folding and Mutant Proteins

Several diseases, such as Alzheimer's disease, Parkinson's disease,Huntington's disease, and others are thought to be the result of, orassociated with misfolding in vivo. In certain embodiments, the presentinvention provides a method of assaying for the presence of proteinmisfolding in a living cell.

Proteins expressed through recombinant means often misfold, particularlyin prokaryotic host cells that lack the processing machinery of aneukaryotic cell. When a protein misfolds, it often becomes less soluble,and may precipitate in the cell as an inclusion body. Additionally,mutations in naturally occurring proteins increase the rate ofmisfolding when endogenously expressed, as well as when exogenouslyexpressed in a recombinant host cell. In certain embodiments, thepresent invention allows various mutations, whether natural or producedby the hand of man, to be assayed for their ability to increase ordecrease protein misfolding in vivo.

1. Fusion Proteins

An aspect of the present invention is the discovery that peptides,polypeptides or proteins, useful for alpha complementation, may bejoined to a larger soluble protein, polypeptide or peptide, wherein thefolding reaction is dominated by the soluble protein, polypeptide orpeptide. The soluble protein, peptide or polypeptide may have the samelength or amino acid sequence as the endogenously produced protein,polypeptide or peptide. In other embodiments, the soluble protein,peptide or polypeptide may be a truncated protein, protein domain orprotein fragment of a larger peptide chain. For example, the folding ofthe soluble fragments of a membrane embedded or otherwise hydrophobicprotein may be used to create a fusion protein.

Fusion proteins are produced by operatively linking at least one nucleicacid encoding at least one amino acid sequence to at least a secondnucleic acid encoding at least a second amino acid sequence, so that theencoded sequences are translated as a contiguous amino acid sequenceeither in vitro or in vivo. Fusion protein design and expression is wellknown in the art, and methods of fusion protein expression are describedherein, and in references, such as, for example, U.S. Pat. No.5,935,824, incorporated herein by reference.

In certain embodiments, a peptide, polypeptide or protein may be joinedat or near the N-terminal or C-terminal end of a soluble protein,peptide or polypeptide. In certain embodiments, it is contemplated thatthe alpha complementing peptide or polypeptide may be attached to thesoluble protein, peptide or polypeptide via a linker moiety. One suchlinker is another peptide, such as described in U.S. Pat. No. 5,990,275,incorporated herein by reference.

2. Mutagenesis

Where employed, mutagenesis will be accomplished by a variety ofstandard, mutagenic procedures. Mutation is the process whereby changesoccur in the quantity or structure of an organism. Mutation can involvemodification of the nucleotide sequence of a single gene, blocks ofgenes or whole chromosome. Changes in single genes may be theconsequence of point mutations which involve the removal, addition orsubstitution of a single nucleotide base within a DNA sequence, or theymay be the consequence of changes involving the insertion or deletion oflarge numbers of nucleotides.

Mutations can arise spontaneously as a result of events such as errorsin the fidelity of DNA replication or the movement of transposablegenetic elements (transposons) within the genome. They also are inducedfollowing exposure to chemical or physical mutagens. Suchmutation-inducing agents include ionizing radiations, ultraviolet lightand a diverse array of chemical such as alkylating agents and polycyclicaromatic hydrocarbons all of which are capable of interacting eitherdirectly or indirectly (generally following some metabolicbiotransformations) with nucleic acids. The DNA lesions induced by suchenvironmental agents may lead to modifications of base sequence when theaffected DNA is replicated or repaired and thus to a mutation. Mutationalso can be site-directed through the use of particular targetingmethods.

a. Random Mutagenesis

i) Insertional Mutagenesis

Insertional mutagenesis is based on the inactivation of a gene viainsertion of a known DNA fragment. Because it involves the insertion ofsome type of DNA fragment, the mutations generated are generallyloss-of-function, rather than gain-of-function mutations. However, thereare several examples of insertions generating gain-of-function mutations(Oppenheimer et al. 1991). Insertion mutagenesis has been verysuccessful in bacteria and Drosophila (Cooley et al. 1988) and recentlyhas become a powerful tool in corn (Schmidt et al. 1987); Arabidopsis;(Marks et al., 1991; Koncz et al. 1990); and Antirrhinum (Sommer et al.1990).

Transposable genetic elements are DNA sequences that can move(transpose) from one place to another in the genome of a cell. The firsttransposable elements to be recognized were the Activator/Dissociationelements of Zea mays. Since then, they have been identified in a widerange of organisms, both prokaryotic and eukaryotic.

Transposable elements in the genome are characterized by being flankedby direct repeats of a short sequence of DNA that has been duplicatedduring transposition and is called a target site duplication. Virtuallyall transposable elements whatever their type, and mechanism oftransposition, make such duplications at the site of their insertion. Insome cases the number of bases duplicated is constant, in other cases itmay vary with each transposition event. Most transposable elements haveinverted repeat sequences at their termini. these terminal invertedrepeats may be anything from a few bases to a few hundred bases long andin many cases they are known to be necessary for transposition.

Prokaryotic transposable elements have been most studied in E. coli andGram negative bacteria, but also are present in Gram positive bacteria.They are generally termed insertion sequences if they are less thanabout 2 kB long, or transposons if they are longer. Bacteriophages suchas mu and D108, which replicate by transposition, make up a third typeof transposable element. elements of each type encode at least onepolypeptide a transposase, required for their own transposition.Transposons often further include genes coding for function unrelated totransposition, for example, antibiotic resistance genes.

Transposons can be divided into two classes according to theirstructure. First, compound or composite transposons have copies of aninsertion sequence element at each end, usually in an invertedorientation. These transposons require transposases encoded by one oftheir terminal IS elements. The second class of transposon have terminalrepeats of about 30 base pairs and do not contain sequences from ISelements.

Transposition usually is either conservative or replicative, although insome cases it can be both. In replicative transposition, one copy of thetransposing element remains at the donor site, and another is insertedat the target site. In conservative transposition, the transposingelement is excised from one site and inserted at another.

Eukaryotic elements also can be classified according to their structureand mechanism of transportation. The primary distinction is betweenelements that transpose via an RNA intermediate, and elements thattranspose directly from DNA to DNA.

Elements that transpose via an RNA intermediate often are referred to asretrotransposons, and their most characteristic feature is that theyencode polypeptides that are believed to have reverse transcriptionaseactivity. There are two types of retrotransposon. Some resemble theintegrated proviral DNA of a retrovirus in that they have long directrepeat sequences, long terminal repeats (LTRs), at each end. Thesimilarity between these retrotransposons and proviruses extends totheir coding capacity. They contain sequences related to the gag and polgenes of a retrovirus, suggesting that they transpose by a mechanismrelated to a retroviral life cycle. Retrotransposons of the second typehave no terminal repeats. They also code for gag- and pol-likepolypeptides and transpose by reverse transcription of RNAintermediates, but do so by a mechanism that differs from that orretrovirus-like elements. Transposition by reverse transcription is areplicative process and does not require excision of an element from adonor site.

Transposable elements are an important source of spontaneous mutations,and have influenced the ways in which genes and genomes have evolved.They can inactivate genes by inserting within them, and can cause grosschromosomal rearrangements either directly, through the activity oftheir transposases, or indirectly, as a result of recombination betweencopies of an element scattered around the genome. Transposable elementsthat excise often do so imprecisely and may produce alleles coding foraltered gene products if the number of bases added or deleted is amultiple of three.

Transposable elements themselves may evolve in unusual ways. If theywere inherited like other DNA sequences, then copies of an element inone species would be more like copies in closely related species thancopies in more distant species. This is not always the case, suggestingthat transposable elements are occasionally transmitted horizontallyfrom one species to another.

ii) Chemical Mutagenesis

Chemical mutagenesis offers certain advantages, such as the ability tofind a full range of mutant alleles with degrees of phenotypic severity,and is facile and inexpensive to perform. The majority of chemicalcarcinogens produce mutations in DNA. Benzo[a]pyrene, N-acetoxy-2-acetylaminofluorene and aflotoxin B 1 cause GC to TA transversions in bacteriaand mammalian cells. Benzo[a]pyrene also can produce base substitutionssuch as AT to TA. N-nitroso compounds produce GC to AT transitions.Alkylation of the 04 position of thymine induced by exposure ton-nitrosoureas results in TA to CG transitions.

A high correlation between mutagenicity and carcinogenity is theunderlying assumption behind the Ames test (McCann et al., 1975) whichspeedily assays for mutants in a bacterial system, together with anadded rat liver homogenate, which contains the microsomal cytochromeP450, to provide the metabolic activation of the mutagens where needed.

In vertebrates, several carcinogens have been found to produce mutationin the ras proto-oncogene. N-nitroso-N-methyl urea induces mammary,prostate and other carcinomas in rats with the majority of the tumorsshowing a G to A transition at the second position in codon 12 of theHa-ras oncogene. Benzo[a]pyrene-induced skin tumors contain A to Ttransformation in the second codon of the Ha-ras gene.

iii) Radiation Mutagenesis

The integrity of biological molecules is degraded by the ionizingradiation. Adsorption of the incident energy leads to the formation ofions and free radicals, and breakage of some covalent bonds.Susceptibility to radiation damage appears quite variable betweenmolecules, and between different crystalline forms of the same molecule.It depends on the total accumulated dose, and also on the dose rate (asonce free radicals are present, the molecular damage they cause dependson their natural diffusion rate and thus upon real time). Damage isreduced and controlled by making the sample as cold as possible.

Ionizing radiation causes DNA damage and cell killing, generallyproportional to the dose rate. Ionizing radiation has been postulated toinduce multiple biological effects by direct interaction with DNA, orthrough the formation of free radical species leading to DNA damage.These effects include gene mutations, malignant transformation, and cellkilling. Although ionizing radiation has been demonstrated to induceexpression of certain DNA repair genes in some prokaryotic and lowereukaryotic cells, little is known about the effects of ionizingradiation on the regulation of mammalian gene expression (Borek, 1985).Several studies have described changes in the pattern of proteinsynthesis observed after irradiation of mammalian cells. For example,ionizing radiation treatment of human malignant melanoma cells isassociated with induction of several unidentified proteins (Boothman etal., 1989). Synthesis of cyclin and co-regulated polypeptides issuppressed by ionizing radiation in rat REF52 cells, but not inoncogene-transformed REF52 cell lines (Lambert and Borek, 1988). Otherstudies have demonstrated that certain growth factors or cytokines maybe involved in x-ray-induced DNA damage. In this regard,platelet-derived growth factor is released from endothelial cells afterirradiation (Witte, et al., 1989).

In the present invention, the term “ionizing radiation” means radiationcomprising particles or photons that have sufficient energy or canproduce sufficient energy via nuclear interactions to produce ionization(gain or loss of electrons). An exemplary and preferred ionizingradiation is an x-radiation. The amount of ionizing radiation needed ina given cell generally depends upon the nature of that cell. Typically,an effective expression-inducing dose is less than a dose of ionizingradiation that causes cell damage or death directly. Means fordetermining an effective amount of radiation are well known in the art.

In a certain embodiments, an effective expression inducing amount isfrom about 2 to about 30 Gray (Gy) administered at a rate of from about0.5 to about 2 Gy/minute. Even more preferably, an effective expressioninducing amount of ionizing radiation is from about 5 to about 15 Gy. Inother embodiments, doses of 2-9 Gy are used in single doses. Aneffective dose of ionizing radiation may be from 10 to 100 Gy, with 15to 75 Gy being preferred, and 20 to 50 Gy being more preferred.

Any suitable means for delivering radiation to a tissue may be employedin the present invention in addition to external means. For example,radiation may be delivered by first providing a radiolabeled antibodythat immunoreacts with an antigen of the tumor, followed by deliveringan effective amount of the radiolabeled antibody to the tumor. Inaddition, radioisotopes may be used to deliver ionizing radiation to atissue or cell.

iv) In Vitro Scanning Mutagenesis

Random mutagenesis also may be introduced using error prone PCR (Cadwelland Joyce, 1992). The rate of mutagenesis may be increased by performingPCR in multiple tubes with dilutions of templates.

One particularly useful mutagenesis technique is alanine scanningmutagenesis in which a number of residues are substituted individuallywith the amino acid alanine so that the effects of losing side-chaininteractions can be determined, while minimizing the risk of large-scaleperturbations in protein conformation (Cunningham et al., 1989).

In recent years, techniques for estimating the equilibrium constant forligand binding using minuscule amounts of protein have been developed(Blackburn et al., 1991; U.S. Pat. Nos. 5,221,605 and 5,238,808). Theability to perform functional assays with small amounts of material canbe exploited to develop highly efficient, in vitro methodologies for thesaturation mutagenesis of antibodies. The inventors bypassed cloningsteps by combining PCR mutagenesis with coupled in vitrotranscription/translation for the high throughput generation of proteinmutants. Here, the PCR products are used directly as the template forthe in vitro transcription/translation of the mutant single chainantibodies. Because of the high efficiency with which all 19 amino acidsubstitutions can be generated and analyzed in this way, it is nowpossible to perform saturation mutagenesis on numerous residues ofinterest, a process that can be described as in vitro scanningsaturation mutagenesis (Burks et al., 1997).

In vitro scanning saturation mutagenesis provides a rapid method forobtaining a large amount of structure-function information including:(i) identification of residues that modulate ligand binding specificity,(ii) a better understanding of ligand binding based on theidentification of those amino acids that retain activity and those thatabolish activity at a given location, (iii) an evaluation of the overallplasticity of an active site or protein subdomain, (iv) identificationof amino acid substitutions that result in increased binding.

v) Random Mutagenesis by Fragmentalion and Reassmbly

A method for generating libraries of displayed polypeptides is describedin U.S. Pat. No. 5,380,721. The method comprises obtainingpolynucleotide library members, pooling and fragmenting thepolynucleotides, and reforming fragments therefrom, performing PCRamplification, thereby homologously recombining the fragments to form ashuffled pool of recombined polynucleotides.

b. Site-Directed Mutagenesis

Structure-guided site-specific mutagenesis represents a powerful toolfor the dissection and engineering of protein-ligand interactions. Thetechnique provides for the preparation and testing of sequence variantsby introducing one or more nucleotide sequence changes into a selectedDNA.

Site-specific mutagenesis uses specific oligonucleotide sequences whichencode the DNA sequence of the desired mutation, as well as a sufficientnumber of adjacent, unmodified nucleotides. In this way, a primersequence is provided with sufficient size and complexity to form astable duplex on both sides of the deletion junction being traversed. Aprimer of about 17 to 25 nucleotides in length is preferred, with about5 to 10 residues on both sides of the junction of the sequence beingaltered.

The technique typically employs a bacteriophage vector that exists inboth a single-stranded and double-stranded form. Vectors useful insite-directed mutagenesis include vectors such as the M13 phage. Thesephage vectors are commercially available and their use is generally wellknown to those skilled in the art. Double-stranded plasmids are alsoroutinely employed in site-directed mutagenesis, which eliminates thestep of transferring the gene of interest from a phage to a plasmid.

In general, one first obtains a single-stranded vector, or melts twostrands of a double-stranded vector, which includes within its sequencea DNA sequence encoding the desired protein or genetic element. Anoligonucleotide primer bearing the desired mutated sequence,synthetically prepared, is then annealed with the single-stranded DNApreparation, taking into account the degree of mismatch when selectinghybridization conditions. The hybridized product is subjected to DNApolymerizing enzymes such as E. coli polymerase I (Klenow fragment) inorder to complete the synthesis of the mutation-bearing strand. Thus, aheteroduplex is formed, wherein one strand encodes the originalnon-mutated sequence, and the second strand bears the desired mutation.This heteroduplex vector is then used to transform appropriate hostcells, such as E. coli cells, and clones are selected that includerecombinant vectors bearing the mutated sequence arrangement.

Comprehensive information on the functional significance and informationcontent of a given residue of protein can best be obtained by saturationmutagenesis in which all 19 amino acid substitutions are examined. Theshortcoming of this approach is that the logistics of multiresiduesaturation mutagenesis are daunting (Warren et al., 1996, Zeng et al.,1996; Yelton et al., 1995; Hilton et al., 1996). Hundreds, and possiblyeven thousands, of site specific mutants must be studied. However,improved techniques make production and rapid screening of mutants muchmore straightforward. See also, U.S. Pat. Nos. 5,798,208 and 5,830,650,for a description of “walk-through” mutagenesis.

Other methods of site-directed mutagenesis are disclosed in U.S. Pat.Nos. 5,220,007; 5,284,760; 5,354,670; 5,366,878; 5,389,514; 5,635,377;and 5,789,166.

B. Protein Expression

1. Vectors

Once the soluble protein, polypeptide or peptide encoding sequence(s)and alpha complementing protein, polypeptide or peptide encodingsequence(s) are selected, they may be operatively expressed in arecombinant vector. The expression may be in vivo or in vitro, to assaythe refolding and complementation process. The term “vector” is used torefer to a carrier nucleic acid molecule into which a nucleic acidsequence can be inserted for introduction into a cell where it can bereplicated. A nucleic acid sequence can be “exogenous,” which means thatit is foreign to the cell into which the vector is being introduced orthat the sequence is homologous to a sequence in the cell but in aposition within the host cell nucleic acid in which the sequence isordinarily not found. Vectors include plasmids, cosmids, viruses(bacteriophage, animal viruses, and plant viruses), and artificialchromosomes (e.g., YACs). One of skill in the art would be well equippedto construct a vector through standard recombinant techniques, which aredescribed in Sambrook et al., 1989 and Ausubel et al., 1994, bothincorporated herein by reference.

The term “expression vector” refers to a vector containing a nucleicacid sequence coding for at least part of a gene product capable ofbeing transcribed. In some cases, RNA molecules are then translated intoa protein, polypeptide, or peptide. In other cases, these sequences arenot translated, for example, in the production of antisense molecules orribozymes. Expression vectors can contain a variety of “controlsequences,” which refer to nucleic acid sequences necessary for thetranscription and possibly translation of an operably linked codingsequence in a particular host organism. In addition to control sequencesthat govern transcription and translation, vectors and expressionvectors may contain nucleic acid sequences that serve other functions aswell and are described infra.

a. Promoters and Enhancers

A “promoter” is a control sequence that is a region of a nucleic acidsequence at which initiation and rate of transcription are controlled.It may contain genetic elements at which regulatory proteins andmolecules may bind such as RNA polymerase and other transcriptionfactors. The phrases “operatively positioned,” “operatively linked,”“under control,” and “under transcriptional control” mean that apromoter is in a correct functional location and/or orientation inrelation to a nucleic acid sequence to control transcriptionalinitiation and/or expression of that sequence. A promoter may or may notbe used in conjunction with an “enhancer,” which refers to a cis-actingregulatory sequence involved in the transcriptional activation of anucleic acid sequence.

A promoter may be one naturally associated with a gene or sequence, asmay be obtained by isolating the 5′ non-coding sequences locatedupstream of the coding segment and/or exon. Such a promoter can bereferred to as “endogenous.” Similarly, an enhancer may be one naturallyassociated with a nucleic acid sequence, located either downstream orupstream of that sequence. Alternatively, certain advantages will begained by positioning the coding nucleic acid segment under the controlof a recombinant or heterologous promoter, which refers to a promoterthat is not normally associated with a nucleic acid sequence in itsnatural environment. A recombinant or heterologous enhancer refers alsoto an enhancer not normally associated with a nucleic acid sequence inits natural environment. Such promoters or enhancers may includepromoters or enhancers of other genes, and promoters or enhancersisolated from any other prokaryotic, viral, or eukaryotic cell, andpromoters or enhancers not “naturally occurring,” i.e., containingdifferent elements of different transcriptional regulatory regions,and/or mutations that alter expression. In addition to producing nucleicacid sequences of promoters and enhancers synthetically, sequences maybe produced using recombinant cloning and/or nucleic acid amplificationtechnology, including PCR™, in connection with the compositionsdisclosed herein (see U.S. Pat. No. 4,683,202, U.S. Pat. No. 5,928,906,each incorporated herein by reference). Furthermore, it is contemplatedthe control sequences that direct transcription and/or expression ofsequences within non-nuclear organelles such as mitochondria,chloroplasts, and the like, can be employed as well.

Naturally, it will be important to employ a promoter and/or enhancerthat effectively directs the expression of the DNA segment in the celltype, organelle, and organism chosen for expression. Those of skill inthe art of molecular biology generally know the use of promoters,enhancers, and cell type combinations for protein expression, forexample, see Sambrook et al. (1989), incorporated herein by reference.The promoters employed may be constitutive, tissue-specific, inducible,and/or useful under the appropriate conditions to direct high levelexpression of the introduced DNA segment, such as is advantageous in thelarge-scale production of recombinant proteins and/or peptides. Thepromoter may be heterologous or endogenous.

Tables 1 lists several elements/promoters that may be employed, in thecontext of the present invention, to regulate the expression of a gene.This list is not intended to be exhaustive of all the possible elementsinvolved in the promotion of expression but, merely, to be exemplarythereof. Table 2 provides examples of inducible elements, which areregions of a nucleic acid sequence that can be activated in response toa specific stimulus. TABLE 1 Promoter and/or Enhancer Promoter/EnhancerReferences Immunoglobulin Heavy Chain Banerji et al., 1983; Gilles etal., 1983; Grosschedl et al., 1985; Atchinson et al., 1986, 1987; Imleret al., 1987; Weinberger et al., 1984; Kiledjian et al., 1988; Porton etal.; 1990 Immunoglobulin Light Chain Queen et al., 1983; Picard et al.,1984 T-Cell Receptor Luria et al., 1987; Winoto et al., 1989; Redondo etal.; 1990 HLA DQ a and/or DQ β Sullivan et al., 1987 β-InterferonGoodbourn et al., 1986; Fujita et al., 1987; Goodbourn et al., 1988Interleukin-2 Greene et al., 1989 Interleukin-2 Receptor Greene et al.,1989; Lin et al., 1990 MHC Class II 5 Koch et al., 1989 MHC Class IIHLA-Dra Sherman et al., 1989 β-Actin Kawamoto et al., 1988; Ng et al.;1989 Muscle Creatine Kinase (MCK) Jaynes et al., 1988; Horlick et al.,1989; Johnson et al., 1989 Prealbumin (Transthyretin) Costa et al., 1988Elastase I Ornitz et al., 1987 Metallothionein (MTII) Karin et al.,1987; Culotta et al., 1989 Collagenase Pinkert et al., 1987; Angel etal., 1987 Albumin Pinkert et al., 1987; Tronche et al., 1989, 1990α-Fetoprotein Godbout et al., 1988; Campere et al., 1989 t-Globin Bodineet al., 1987; Perez-Stable et al., 1990 β-Globin Trudel et al., 1987c-fos Cohen et al., 1987 c-HA-ras Triesman, 1986; Deschamps et al., 1985Insulin Edlund et al., 1985 Neural Cell Adhesion Molecule Hirsh et al.,1990 (NCAM) α₁-Antitrypain Latimer et al., 1990 H2B (TH2B) Histone Hwanget al., 1990 Mouse and/or Type I Collagen Ripe et al., 1989Glucose-Regulated Proteins Chang et al., 1989 (GRP94 and GRP78) RatGrowth Hormone Larsen et al., 1986 Human Serum Amyloid A (SAA) Edbrookeet al., 1989 Troponin I (TN I) Yutzey et al., 1989 Platelet-DerivedGrowth Factor Pech et al., 1989 (PDGF) Duchenne Muscular DystrophyKlamut et al., 1990 SV40 Banerji et al., 1981; Moreau et al., 1981;Sleigh et al., 1985; Firak et al., 1986; Herr et al., 1986; Imbra etal., 1986; Kadesch et al., 1986; Wang et al., 1986; Ondek et al., 1987;Kuhl et al., 1987; Schaffner et al., 1988 Polyoma Swartzendruber et al.,1975; Vasseur et al., 1980; Katinka et al., 1980, 1981; Tyndell et al.,1981; Dandolo et al., 1983; de Villiers et al., 1984; Hen et al., 1986;Satake et al., 1988; Campbell and/or Villarreal, 1988 RetrovirusesKriegler et al., 1982, 1983; Levinson et al., 1982; Kriegler et al.,1983, 1984a, b, 1988; Bosze et al., 1986; Miksicek et al., 1986;Celander et al., 1987; Thiesen et al., 1988; Celander et al., 1988; Cholet al., 1988; Reisman et al., 1989 Papilloma Virus Campo et al., 1983;Lusky et al., 1983; Spandidos and/or Wilkie, 1983; Spalholz et al.,1985; Lusky et al., 1986; Cripe et al., 1987; Gloss et al., 1987;Hirochika et al., 1987; Stephens et al., 1987; Glue et al., 1988Hepatitis B Virus Bulla et al., 1986; Jameel et al., 1986; Shaul et al.,1987; Spandau et al., 1988; Vannice et al., 1988 Human ImmunodeficiencyVirus Muesing et al., 1987; Hauber et al., 1988; Jakobovits et al.,1988; Feng et al., 1988; Takebe et al., 1988; Rosen et al., 1988;Berkhout et al., 1989; Laspia et al., 1989; Sharp et al., 1989; Braddocket al., 1989 Cytomegalovirus (CMV) Weber et al., 1984; Boshart et al.,1985; Foecking et al., 1986 Gibbon Ape Leukemia Virus Holbrook et al.,1987; Quinn et al., 1989

TABLE 2 Inducible Elements Element Inducer References MT II PhorbolEster (TFA) Palmiter et al., 1982; Heavy metals Haslinger et al., 1985;Searle et al., 1985; Stuart et al., 1985; Imagawa et al., 1987, Karin etal., 1987; Angel et al., 1987b; McNeall et al., 1989 MMTV (mouseGlucocorticoids Huang et al., 1981; Lee mammary et al., 1981; Majors ettumor virus) al., 1983; Chandler et al., 1983; Lee et al., 1984; Pontaet al., 1985; Sakai et al., 1988 β-Interferon Poly(rI)x Tavernier etal., 1983 Poly(rc) Adenovirus 5 E2 E1A Imperiale et al., 1984Collagenase Phorbol Ester (TPA) Angel et al., 1987a Stromelysin PhorbolEster (TPA) Angel et al., 1987b SV40 Phorbol Ester (TPA) Angel et al.,1987b Murine MX Gene Interferon, Hug et al., 1988 Newcastle DiseaseVirus GRP78 Gene A23187 Resendez et al., 1988 α-2- IL-6 Kunz et al.,1989 Macroglobulin Vimentin Serum Rittling et al., 1989 MHC Class IInterferon Blanar et al., 1989 Gene H-2κb HSP70 E1A, SV40 Large T Tayloret al., 1989, Antigen 1990a, 1990b Proliferin Phorbol Ester-TPA Mordacqet al., 1989 Tumor Necrosis PMA Hensel et al., 1989 Factor ThyroidStimulating Thyroid Hormone Chatterjee et al., 1989 Hormone α Gene

The identity of tissue-specific promoters or elements, as well as assaysto characterize their activity, is well known to those of skill in theart. Examples of such regions include the human LIMK2 gene (Nomoto etal. 1999), the somatostatin receptor 2 gene (Kraus et al., 1998), murineepididymal retinoic acid-binding gene (Lareyre et al., 1999), human CD4(Zhao-Emonet et al., 1998), mouse alpha2 (XI) collagen (Tsumaki, et al.,1998), DIA dopamine receptor gene (Lee, et al., 1997), insulin-likegrowth factor II (Wu et al., 1997), human platelet endothelial celladhesion molecule-1 (Almendro et al., 1996).

b. Initiation Signals and Internal Ribosome Binding Sites

A specific initiation signal also may be required for efficienttranslation of coding sequences. These signals include the ATGinitiation codon or adjacent sequences. Exogenous translational controlsignals, including the ATG initiation codon, may need to be provided.One of ordinary skill in the art would readily be capable of determiningthis and providing the necessary signals. It is well known that theinitiation codon must be “in-frame” with the reading frame of thedesired coding sequence to ensure translation of the entire insert. Theexogenous translational control signals and initiation codons can beeither natural or synthetic. The efficiency of expression may beenhanced by the inclusion of appropriate transcription enhancerelements.

In certain embodiments of the invention, the use of internal ribosomeentry sites (IRES) elements are used to create multigene, orpolycistronic, messages. IRES elements are able to bypass the ribosomescanning model of 5′ methylated Cap dependent translation and begintranslation at internal sites (Pelletier and Sonenberg, 1988). IRESelements from two members of the picomavirus family (polio andencephalomyocarditis) have been described (Pelletier and Sonenberg,1988), as well an IRES from a mammalian message (Macejak and Sarnow,1991). IRES elements can be linked to heterologous open reading frames.Multiple open reading frames can be transcribed together, each separatedby an IRES, creating polycistronic messages. By virtue of the IRESelement, each open reading frame is accessible to ribosomes forefficient translation. Multiple genes can be efficiently expressed usinga single promoter/enhancer to transcribe a single message (see U.S. Pat.Nos. 5,925,565 and 5,935,819, herein incorporated by reference).

c. Multiple Cloning Sites

Vectors can include a multiple cloning site (MCS), which is a nucleicacid region that contains multiple restriction enzyme sites, any ofwhich can be used in conjunction with standard recombinant technology todigest the vector. (See Carbonelli et al., 1999, Levenson et al., 1998,and Cocea, 1997, incorporated herein by reference.) “Restriction enzymedigestion” refers to catalytic cleavage of a nucleic acid molecule withan enzyme that functions only at specific locations in a nucleic acidmolecule. Many of these restriction enzymes are commercially available.Use of such enzymes is widely understood by those of skill in the art.Frequently, a vector is linearized or fragmented using a restrictionenzyme that cuts within the MCS to enable exogenous sequences to beligated to the vector. “Ligation” refers to the process of formingphosphodiester bonds between two nucleic acid fragments, which may ormay not be contiguous with each other. Techniques involving restrictionenzymes and ligation reactions are well known to those of skill in theart of recombinant technology.

d. Splicing Sites

Most transcribed eukaryotic RNA molecules will undergo RNA splicing toremove introns from the primary transcripts. Vectors containing genomiceukaryotic sequences may require donor and/or acceptor splicing sites toensure proper processing of the transcript for protein expression. (SeeChandler et al., 1997, herein incorporated by reference.)

e. Polyadenylation Signals

In expression, one will typically include a polyadenylation signal toeffect proper polyadenylation of the transcript. The nature of thepolyadenylation signal is not believed to be crucial to the successfulpractice of the invention, and/or any such sequence may be employed.Preferred embodiments include the SV40 polyadenylation signal and/or thebovine growth hormone polyadenylation signal, convenient and/or known tofunction well in various target cells. Also contemplated as an elementof the expression cassette is a transcriptional termination site. Theseelements can serve to enhance message levels and/or to minimize readthrough from the cassette into other sequences.

f. Origins of Replication

In order to propagate a vector in a host cell, it may contain one ormore origins of replication sites (often termed “ori”), which is aspecific nucleic acid sequence at which replication is initiated.Alternatively an autonomously replicating sequence (ARS) can be employedif the host cell is yeast.

g. Selectable and Screenable Markers

In certain embodiments of the invention, the cells contain nucleic acidconstruct of the present invention, a cell may be identified in vitro orin vivo by including a marker in the expression vector. Such markerswould confer an identifiable change to the cell permitting easyidentification of cells containing the expression vector. Generally, aselectable marker is one that confers a property that allows forselection. A positive selectable marker is one in which the presence ofthe marker allows for its selection, while a negative selectable markeris one in which its presence prevents its selection. An example of apositive selectable marker is a drug resistance marker.

Usually the inclusion of a drug selection marker aids in the cloning andidentification of transformants, for example, genes that conferresistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin andhistidinol are useful selectable markers. In addition to markersconferring a phenotype that allows for the discrimination oftransformants based on the implementation of conditions, other types ofmarkers including screenable markers such as GFP, whose basis iscolorimetric analysis, are also contemplated. Alternatively, screenableenzymes such as herpes simplex virus thymidine kinase (tk) orchloramphenicol acetyltransferase (CAT) may be utilized. One of skill inthe art would also know how to employ immunologic markers, possibly inconjunction with FACS analysis. The marker used is not believed to beimportant, so long as it is capable of being expressed simultaneouslywith the nucleic acid encoding a gene product. Further examples ofselectable and screenable markers are well known to one of skill in theart.

2. Host Cells

As used herein, the terms “cell,” “cell line,” and “cell culture” may beused interchangeably. All of these term also include their progeny,which is any and all subsequent generations. It is understood that allprogeny may not be identical due to deliberate or inadvertent mutations.In the context of expressing a heterologous nucleic acid sequence, “hostcell” refers to a prokaryotic or eukaryotic cell, and it includes anytransformable organisms that is capable of replicating a vector and/orexpressing a heterologous gene encoded by a vector. A host cell can, andhas been, used as a recipient for vectors. A host cell may be“transfected” or “transformed,” which refers to a process by whichexogenous nucleic acid is transferred or introduced into the host cell.A transformed cell includes the primary subject cell and its progeny.

Host cells may be derived from prokaryotes or eukaryotes, depending uponwhether the desired result is replication of the vector or expression ofpart or all of the vector-encoded nucleic acid sequences. Prokaryotesinclude gram negative or positive cells. Numerous cell lines andcultures are available for use as a host cell, and they can be obtainedthrough the American Type Culture Collection (ATCC), which is anorganization that serves as an archive for living cultures and geneticmaterials (www.atcc.org). An appropriate host can be determined by oneof skill in the art based on the vector backbone and the desired result.A plasmid or cosmid, for example, can be introduced into a prokaryotehost cell for replication of many vectors. Bacterial cells used as hostcells for vector replication and/or expression include DH5α, JM109, andKC8, as well as a number of commercially available bacterial hosts suchas SURE® Competent Cells and SOLOPACK™ Gold Cells (STRATAGENE®, LaJolla). Alternatively, bacterial cells such as E. coli LE392 could beused as host cells for phage viruses.

Examples of eukaryotic host cells for replication and/or expression of avector include C. elegans, HeLa, NIH3T3, Jurkat, 293, Cos, CHO, Saos,yeast, nematodes, insect cells, and PC12. Many host cells from variouscell types and organisms are available and would be known to one ofskill in the art. Similarly, a viral vector may be used in conjunctionwith either a eukaryotic or prokaryotic host cell, particularly one thatis permissive for replication or expression of the vector.

Some vectors may employ control sequences that allow it to be replicatedand/or expressed in both prokaryotic and eukaryotic cells. One of skillin the art would further understand the conditions under which toincubate all of the above described host cells to maintain them and topermit replication of a vector. Also understood and known are techniquesand conditions that would allow large-scale production of vectors, aswell as production of the nucleic acids encoded by vectors and theircognate polypeptides, proteins, or peptides.

3. Expression Systems

Turning to the expression of the proteins of the present invention, oncea suitable nucleic acid encoding sequence has been obtained, one mayproceed to prepare an expression system. The engineering of DNAsegment(s) for expression in a prokaryotic or eukaryotic system may beperformed by techniques generally known to those of skill in recombinantexpression.

It is believed that virtually any expression system may be employed inthe expression of the proteins of the present invention. Prokaryote-and/or eukaryote-based systems can be employed for use with the presentinvention to produce nucleic acid sequences, or their cognatepolypeptides, proteins and peptides. Many such systems are commerciallyand widely available.

Both cDNA and genomic sequences are suitable for eukaryotic expression,as the host cell will generally process the genomic transcripts to yieldfunctional mRNA for translation into protein. Generally speaking, it maybe more convenient to employ as the recombinant gene a cDNA version ofthe gene. It is believed that the use of a cDNA version will provideadvantages in that the size of the gene will generally be much smallerand more readily employed to transfect the targeted cell than will agenomic gene, which will typically be up to an order of magnitude ormore larger than the cDNA gene. However, it is contemplated that agenomic version of a particular gene may be employed where desired.

It is contemplated that proteins, polypeptides or peptides may beco-expressed with other selected proteins, polypeptides or peptides,wherein the proteins may be co-expressed in the same cell or gene(s) maybe provided to a cell that already has another selected protein.Co-expression may be achieved by co-transfecting the cell with twodistinct recombinant vectors, each bearing a copy of either of therespective DNA. Alternatively, a single recombinant vector may beconstructed to include the coding regions for both of the proteins,which could then be expressed in cells transfected with the singlevector. In either event, the term “co-expression” herein refers to theexpression of both at least one selected nucleic acid or gene encodingone or more proteins, polypeptides or peptides and at least a secondselected nucleic acid or gene encoding at least one or more secondaryselected proteins, polypeptides or peptides in the same recombinantcell.

It is contemplated that proteins may be expressed in cell systems orgrown in media that enhance protein production. One such system isdescribed in U.S. Pat. No. 5,834,249, incorporated herein by reference.In certain embodiments, the fusion protein may be co-expressed with oneor more proteins that enhance refolding. Such proteins that enhancerefolding include, for example, DsbA or DsbC proteins. A cell systemco-expressing the DsbA or DsbC proteins are described in U.S. Pat. No.5,639,635, incorporated herein by reference. In certain embodiments, itis contemplated that a temperature sensitive expression vector may beused to aid assaying protein folding at lower or higher temperaturesthan many E. coli cell strain's optimum growth at about 37° C. Forexample, a temperature sensitive expression vectors and host cells thatexpress proteins at or below 20° C. is described in U.S. Pat. Nos.5,654,169 and 5,726,039, each incorporated herein by reference.

As used herein, the terms “engineered” and “recombinant” cells or hostcells are intended to refer to a cell into which an exogenous DNAsegment or gene, such as a cDNA or gene encoding at least one protein,polypeptide or peptide has been introduced. Therefore, engineered cellsare distinguishable from naturally occurring cells which do not containa recombinantly introduced exogenous DNA segment or gene. Engineeredcells are thus cells having a gene or genes introduced through the handof man. Recombinant cells include those having an introduced cDNA orgenomic gene, and also include genes positioned adjacent to a promoternot naturally associated with the particular introduced gene.

Certain examples of prokaryotic hosts are E. coli strain RR1, E. coliLE392, E. coli B, E. coli X 1776 (ATCC No. 31537) as well as E. coliW3110 (F-, lambda-, prototrophic, ATCC No. 273325); bacilli such asBacillus subtilis; and other enterobacteriaceae such as Salmonellatyphimurium, Serratia marcescens, and various Pseudomonas species.

In general, plasmid vectors containing replicon and control sequenceswhich are derived from species compatible with the host cell are used inconnection with these hosts. The vector ordinarily carries a replicationsite, as well as marking sequences which are capable of providingphenotypic selection in transformed cells. For example, E. coli is oftentransformed using derivatives of pBR322, a plasmid derived from an E.coli species. pBR322 contains genes for ampicillin and tetracyclineresistance and thus provides easy means for identifying transformedcells. The pBR plasmid, or other microbial plasmid or phage must alsocontain, or be modified to contain, promoters which can be used by themicrobial organism for expression of its own proteins.

In addition, phage vectors containing replicon and control sequencesthat are compatible with the host microorganism can be used astransforming vectors in connection with these hosts. For example, thephage lambda GEM™-11 may be utilized in making a recombinant phagevector which can be used to transform host cells, such as E. coli LE392.

Further useful vectors include pIN vectors (Inouye et al., 1985); andpGEX vectors, for use in generating glutathione S-transferase (GST)soluble fusion proteins for later purification and separation orcleavage. Other suitable fusion proteins are those with β-galactosidase,ubiquitin, and the like.

Promoters that are most commonly used in recombinant DNA constructioninclude the β-lactamase (penicillinase), lactose and tryptophan (trp)promoter systems. While these are the most commonly used, othermicrobial promoters have been discovered and utilized, and detailsconcerning their nucleotide sequences have been published, enablingthose of skill in the art to ligate them functionally with plasmidvectors.

a. Prokaryotic Expression

The following details concerning recombinant protein production inbacterial cells, such as E. coli, are provided by way of exemplaryinformation on recombinant protein production in general, the adaptationof which to a particular recombinant expression system will be known tothose of skill in the art.

Bacterial cells, for example, E. coli, containing the expression vectorare grown in any of a number of suitable media, for example, LB. Theexpression of the recombinant protein may be induced, e.g., by addingIPTG to the media or by switching incubation to a higher temperature.After culturing the bacteria for a further period, generally of between2 and 24 hours, the cells are collected by centrifugation and washed toremove residual media.

The bacterial cells are then lysed, for example, by disruption in a cellhomogenizer and centrifuged to separate the dense inclusion bodies andcell membranes from the soluble cell components. This centrifugation canbe performed under conditions whereby the dense inclusion bodies areselectively enriched by incorporation of sugars, such as sucrose, intothe buffer and centrifugation at a selective speed.

If the recombinant protein is expressed in the inclusion bodies, as isthe case in many instances, these can be washed in any of severalsolutions to remove some of the contaminating host proteins, thensolubilized in solutions containing high concentrations of urea (e.g.8M) or chaotropic agents such as guanidine hydrochloride in the presenceof reducing agents, such as β-mercaptoethanol or DTT (dithiothreitol).

Under some circumstances, it may be advantageous to incubate the proteinfor several hours under conditions suitable for the protein to undergo arefolding process into a conformation which more closely resembles thatof the native protein. Such conditions generally include low proteinconcentrations, less than 500 mg/ml, low levels of reducing agent,concentrations of urea less than 2 M and often the presence of reagentssuch as a mixture of reduced and oxidized glutathione which facilitatethe interchange of disulfide bonds within the protein molecule.

The refolding process can be monitored, for example, by SDS-PAGE, orwith antibodies specific for the native molecule (which can be obtainedfrom animals vaccinated with the native molecule or smaller quantitiesof recombinant protein). Following refolding, the protein can then bepurified further and separated from the refolding mixture bychromatography on any of several supports including ion exchange resins,gel permeation resins or on a variety of affinity columns.

b. Eukaryotic Expression

In addition to micro-organisms, cultures of cells derived frommulticellular organisms may also be used as hosts. In principle, anysuch cell culture is workable, whether from vertebrate or invertebrateculture. In addition to mammalian cells, these include insect cellsystems infected with recombinant virus expression vectors (e.g.,baculovirus); and plant cell systems infected with recombinant virusexpression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaicvirus, TMV) or transformed with recombinant plasmid expression vectors(e.g., Ti plasmid) containing one or more protein, polypeptide orpeptide coding sequences.

For expression in Saccharomyces, the plasmid YRp7, for example, iscommonly used. This plasmid already contains the trp1 gene whichprovides a selection marker for a mutant strain of yeast lacking theability to grow in tryptophan, for example ATCC No. 44076 or PEP4-1. Thepresence of the trp1 lesion as a characteristic of the yeast host cellgenome then provides an effective environment for detectingtransformation by growth in the absence of tryptophan.

Suitable promoting sequences in yeast Vectors include the promoters for3-phosphoglycerate kinase or other glycolytic enzymes, such as enolase,glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvatedecarboxylase, phosphofructokinase, glucose-6-phosphate isomerase,3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase,phosphoglucose isomerase, and glucokinase. In constructing suitableexpression plasmids, the termination sequences associated with thesegenes are also ligated into the expression vector 3′ of the sequencedesired to be expressed to provide polyadenylation of the mRNA andtermination.

Other suitable promoters, which have the additional advantage oftranscription controlled by growth conditions, include the promoterregion for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase,degradative enzymes associated with nitrogen metabolism, and theaforementioned glyceraldehyde-3-phosphate dehydrogenase, and enzymesresponsible for maltose and galactose utilization.

The insect cell/baculovirus system can produce a high level of proteinexpression of a heterologous nucleic acid segment, such as described inU.S. Pat. Nos. 5,871,986, 4,879,236, both herein incorporated byreference, and which can be bought, for example, under the name MAXBAC®2.0 from INVITROGEN® and BACPACK™ BACULOVIRUS EXPRESSION SYSTEM FROMCLONTECH®.

In a useful insect system, Autograph californica nuclear polyhedrosisvirus (AcNPV) is used as a vector to express foreign genes. The virusgrows in Spodoptera frugiperda cells. The protein, polypeptide orpeptide coding sequences are cloned into non-essential regions (forexample the polyhedrin gene) of the virus and placed under control of anAcNPV promoter (for example the polyhedrin promoter). Successfulinsertion of the coding sequences results in the inactivation of thepolyhedrin gene and production of non-occluded recombinant virus (i.e.,virus lacking the proteinaceous coat coded for by the polyhedrin gene).These recombinant viruses are then used to infect Spodoptera frugiperdacells in which the inserted gene is expressed (e.g., U.S. Pat. No.4,215,051, Smith, incorporated herein by reference).

Other examples of expression systems include STRATAGENE®'S COMPLETECONTROL™ Inducible Mammalian Expression System, which involves asynthetic ecdysone-inducible receptor, or its pET Expression System, anE. coli expression system. Another example of an inducible expressionsystem is available from INVITROGEN®, which carries the T-REX™(tetracycline-regulated expression) System, an inducible mammalianexpression system that uses the full-length CMV promoter. INVITROGEN®also provides a yeast expression system called the Pichia methanolicaExpression System, which is designed for high-level production ofrecombinant proteins in the methylotrophic yeast Pichia methanolica. Oneof skill in the art would know how to express a vector, such as anexpression construct, to produce a nucleic acid sequence or its cognatepolypeptide, protein, or peptide.

Examples of useful mammalian host cell lines are VERO and HeLa cells,Chinese hamster ovary (CHO) cell lines, WI 38, BHK, COS-7, 293, HepG2,3T3, RIN and MDCK cell lines. In addition, a host cell strain may bechosen that modulates the expression of the inserted sequences, ormodifies and processes the gene product in the specific fashion desired.Such modifications (e.g., glycosylation) and processing (e.g., cleavage)of protein products may be important for the function of the protein.

Different host cells have characteristic and specific mechanisms for thepost-translational processing and modification of proteins. Appropriatecells lines or host systems can be chosen to ensure the correctmodification and processing of the foreign protein expressed.

Expression vectors for use in mammalian cells ordinarily include anorigin of replication (as necessary), a promoter located in front of thegene to be expressed, along with any necessary ribosome binding sites,RNA splice sites, polyadenylation site, and transcriptional terminatorsequences. The origin of replication may be provided either byconstruction of the vector to include an exogenous origin, such as maybe derived from SV40 or other viral (e.g., Polyoma, Adeno, VSV, BPV)source, or may be provided by the host cell chromosomal replicationmechanism. If the vector is integrated into the host cell chromosome,the latter is often sufficient.

The promoters may be derived from the genome of mammalian cells (e.g.,metallothionein promoter) or from mammalian viruses (e.g., theadenovirus late promoter; the vaccinia virus 7.5K promoter). Further, itis also possible, and may be desirable, to utilize promoter or controlsequences normally associated with the gene sequence(s), provided suchcontrol sequences are compatible with the host cell systems.

A number of viral based expression systems may be utilized, for example,commonly used promoters are derived from polyoma, Adenovirus 2, and mostfrequently Simian Virus 40 (SV40). The early and late promoters of SV40virus are particularly useful because both are obtained easily from thevirus as a fragment which also contains the SV40 viral origin ofreplication. Smaller or larger SV40 fragments may also be used, providedthere is included the approximately 250 bp sequence extending from theHindIII site toward the BglI site located in the viral origin ofreplication.

In cases where an adenovirus is used as an expression vector, the codingsequences may be ligated to an adenovirus transcription/translationcontrol complex, e.g., the late promoter and tripartite leader sequence.This chimeric gene may then be inserted in the adenovirus genome by invitro or in vivo recombination. Insertion in a non-essential region ofthe viral genome (e.g., region E1, E3, or E4) will result in arecombinant virus that is viable and capable of expressing proteins,polypeptides or peptides in infected hosts.

Specific initiation signals may also be required for efficienttranslation of protein, polypeptide or peptide coding sequences. Thesesignals include the ATG initiation codon and adjacent sequences.Exogenous translational control signals, including the ATG initiationcodon, may additionally need to be provided. One of ordinary skill inthe art would readily be capable of determining this and providing thenecessary signals. It is well known that the initiation codon must bein-frame (or in-phase) with the reading frame of the desired codingsequence to ensure translation of the entire insert. These exogenoustranslational control signals and initiation codons can be of a varietyof origins, both natural and synthetic. The efficiency of expression maybe enhanced by the inclusion of appropriate transcription enhancerelements and transcription terminators.

In eukaryotic expression, one will also typically desire to incorporateinto the transcriptional unit an appropriate polyadenylation site (e.g.,5′-AATAAA-3′) if one was not contained within the original clonedsegment. Typically, the poly A addition site is placed about 30 to 2000nucleotides “downstream” of the termination site of the protein at aposition prior to transcription termination.

C. Gene Delivery

The general approach to the aspects of the present invention is toprovide a cell with nucleic acid encoding a fusion protein, polypeptideor peptide and/or a nucleic acid encoding a protein, polypeptide orpeptide whose activity may be altered by complementation with the fusionprotein, thereby permitting a detectable change in the activity of theproteins to take effect. While it is conceivable that the protein(s) maybe delivered directly, a preferred embodiment involves providing anucleic acid encoding the protein(s), polypeptide(s) or peptide(s) tothe cell. Following this provision, the polypeptide(s) are synthesizedby the transcriptional and translational machinery of the cell, as wellas any that may be provided by the expression construct.

In certain embodiments of the invention, the nucleic acid encoding thegene may be stably integrated into the genome of the cell. In yetfurther embodiments, the nucleic acid may be stably maintained in thecell as a separate, episomal segment of DNA. Such nucleic acid segmentsor “episomes” encode sequences sufficient to permit maintenance andreplication independent of or in synchronization with the host cellcycle. How the expression construct is delivered to a cell and where inthe cell the nucleic acid remains is dependent on the type of expressionconstruct employed.

1. DNA Delivery Using Viral Vectors

The ability of certain viruses to infect cells or enter cells viareceptor-mediated endocytosis, and to integrate into host cell genomeand express viral genes stably and efficiently have made them attractivecandidates for the transfer of foreign genes into mammalian cells.Preferred vectors of the present invention will generally be viralvectors.

Although some viruses that can accept foreign genetic material arelimited in the number of nucleotides they can accommodate and in therange of cells they infect, these viruses have been demonstrated tosuccessfully effect gene expression. However, adenoviruses do notintegrate their genetic material into the host genome and therefore donot require host replication for gene expression, making them ideallysuited for rapid, efficient, heterologous gene expression. Techniquesfor preparing replication-defective infective viruses are well known inthe art.

Of course, in using viral delivery systems, one will desire to purifythe virion sufficiently to render it essentially free of undesirablecontaminants, such as defective interfering viral particles orendotoxins and other pyrogens such that it will not cause any untowardreactions in the cell, animal or individual receiving the vectorconstruct. A preferred means of purifying the vector involves the use ofbuoyant density gradients, such as cesium chloride gradientcentrifugation.

a. Adenoviral Vectors

A particular method for delivery of the expression constructs involvesthe use of an adenovirus expression vector. Although adenovirus vectorsare known to have a low capacity for integration into genomic DNA, thisfeature is counterbalanced by the high efficiency of gene transferafforded by these vectors. “Adenovirus expression vector” is meant toinclude those constructs containing adenovirus sequences sufficient to(a) support packaging of the construct and (b) to ultimately express atissue or cell-specific construct that has been cloned therein.

The expression vector comprises a genetically engineered form ofadenovirus. Knowledge of the genetic organization or adenovirus, a 36kb, linear, double-stranded DNA virus, allows substitution of largepieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus andHorwitz, 1992). In contrast to retrovirus, the adenoviral infection ofhost cells does not result in chromosomal integration because adenoviralDNA can replicate in an episomal manner without potential genotoxicity.Also, adenoviruses are structurally stable, and no genome rearrangementhas been detected after extensive amplification.

Adenovirus is particularly suitable for use as a gene transfer vectorbecause of its mid-sized genome, ease of manipulation, high titer, widetarget-cell range and high infectivity. Both ends of the viral genomecontain 100-200 base pair inverted repeats (ITRs), which are ciselements necessary for viral DNA replication and packaging. The early(E) and late (L) regions of the genome contain different transcriptionunits that are divided by the onset of viral DNA replication. The E1region (E1A and E1B) encodes proteins responsible for the regulation oftranscription of the viral genome and a few cellular genes. Theexpression of the E2 region (E2A and E2B) results in the synthesis ofthe proteins for viral DNA replication. These proteins are involved inDNA replication, late gene expression and host cell shut-off (Renan,1990). The products of the late genes, including the majority of theviral capsid proteins, are expressed only after significant processingof a single primary transcript issued by the major late promoter (MLP).The MLP (located at 16.8 m.u.) is particularly efficient during the latephase of infection, and all the mRNA's issued from this promoter possessa 5′-tripartite leader (TPL) sequence which makes them preferred mRNA'sfor translation.

In a current system, recombinant adenovirus is generated from homologousrecombination between shuttle vector and provirus vector. Due to thepossible recombination between two proviral vectors, wild-typeadenovirus may be generated from this process. Therefore, it is criticalto isolate a single clone of virus from an individual plaque and examineits genomic structure.

Generation and propagation of the current adenovirus vectors, which arereplication deficient, depend on a unique helper cell line, designated293, which was transformed from human embryonic kidney cells by Ad5 DNAfragments and constitutively expresses E1 proteins (E1A and E1B; Grahamet al., 1977). Since the E3 region is dispensable from the adenovirusgenome (Jones and Shenk, 1978), the current adenovirus vectors, with thehelp of 293 cells, carry foreign DNA in either the E1, the D3 or bothregions (Graham and Prevec, 1991). Recently, adenoviral vectorscomprising deletions in the E4 region have been described (U.S. Pat. No.5,670,488, incorporated herein by reference).

In nature, adenovirus can package approximately 105% of the wild-typegenome (Ghosh-Choudhury et al., 1987), providing capacity for about 2extra kb of DNA. Combined with the approximately 5.5 kb of DNA that isreplaceable in the E1 and E3 regions, the maximum capacity of thecurrent adenovirus vector is under 7.5 kb, or about 15% of the totallength of the vector. More than 80% of the adenovirus viral genomeremains in the vector backbone.

Helper cell lines may be derived from human cells such as humanembryonic kidney cells, muscle cells, hematopoietic cells or other humanembryonic mesenchymal or epithelial cells. Alternatively, the helpercells may be derived from the cells of other mammalian species that arepermissive for human adenovirus. Such cells include, e.g., Vero cells orother monkey embryonic mesenchymal or epithelial cells. As stated above,the preferred helper cell line is 293.

Racher et al. (1995) disclosed improved methods for culturing 293 cellsand propagating adenovirus. In one format, natural cell aggregates aregrown by inoculating individual cells into 1 liter siliconized spinnerflasks (Techne, Cambridge, UK) containing 100-200 ml of medium.Following stirring at 40 rpm, the cell viability is estimated withtrypan blue. In another format, Fibra-Cel microcarriers (Bibby Sterlin,Stone, UK) (5 g/l) is employed as follows. A cell inoculum, resuspendedin 5 ml of medium, is added to the carrier (50 ml) in a 250 mlErlenmeyer flask and left stationary, with occasional agitation, for 1to 4 h. The medium is then replaced with 50 ml of fresh medium andshaking initiated. For virus production, cells are allowed to grow toabout 80% confluence, after which time the medium is replaced (to 25% ofthe final volume) and adenovirus added at an MOI of 0.05. Cultures areleft stationary overnight, following which the volume is increased to100% and shaking commenced for another 72 h.

Other than the requirement that the adenovirus vector be replicationdefective, or at least conditionally defective, the nature of theadenovirus vector is not believed to be crucial to the successfulpractice of the invention. The adenovirus may be of any of the 42different known serotypes or subgroups A-F. Adenovirus type 5 ofsubgroup C is the preferred starting material in order to obtain theconditional replication-defective adenovirus vector for use in thepresent invention. This is because Adenovirus type 5 is a humanadenovirus about which a great deal of biochemical and geneticinformation is known, and it has historically been used for mostconstructions employing adenovirus as a vector.

As stated above, the typical vector according to the present inventionis replication defective and will not have an adenovirus E1 region.Thus, it will be most convenient to introduce the transforming constructat the position from which the E1-coding sequences have been removed.However, the position of insertion of the construct within theadenovirus sequences is not critical to the invention. Thepolynucleotide encoding the gene of interest may also be inserted inlieu of the deleted E3 region in E3 replacement vectors as described byKarlsson et al. (1986) or in the E4 region where a helper cell line orhelper virus complements the E4 defect.

Adenovirus growth and manipulation is known to those of skill in theart, and exhibits broad host range in vitro and in vivo. This group ofviruses can be obtained in high titers, e.g., 10⁹ to 10¹¹ plaque-formingunits per ml, and they are highly infective. The life cycle ofadenovirus does not require integration into the host cell genome. Theforeign genes delivered by adenovirus vectors are episomal and,therefore, have low genotoxicity to host cells.

Adenovirus vectors have been used in eukaryotic gene expression (Levreroet al., 1991; Gomez-Foix et al., 1992) and vaccine development (Grunhausand Horwitz, 1992; Graham and Prevec, 1992). Recombinant adenovirus andadeno-associated virus (see below) can both infect and transducenon-dividing human primary cells.

b. AAV Vectors

Adeno-associated virus (AAV) is an attractive vector system for use inthe cell transduction of the present invention as it has a highfrequency of integration and it can infect nondividing cells, thusmaking it useful for delivery of genes into mammalian cells, forexample, in tissue culture (Muzyczka, 1992) or in vivo. AAV has a broadhost range for infectivity (Tratschin et al., 1984; Laughlin et al.,1986; Lebkowski et al., 1988; McLaughlin et al., 1988). Detailsconcerning the generation and use of rAAV vectors are described in U.S.Pat. No. 5,139,941 and U.S. Pat. No. 4,797,368, each incorporated hereinby reference.

Studies demonstrating the use of AAV in gene delivery include LaFace etal. (1988); Zhou et al. (1993); Flotte et al. (1993); and Walsh et al.(1994). Recombinant AAV vectors have been used successfully for in vitroand in vivo transduction of marker genes (Kaplitt et al., 1994;Lebkowski et al, 1988; Samulski et al, 1989; Yoder et al., 1994; Zhou etal, 1994; Hermonat and Muzyczka, 1984; Tratschin et al., 1985;McLaughlin et al, 1988) and genes involved in human diseases (Flotte etal., 1992; Luo et al., 1994; Ohi et al., 1990; Walsh et al., 1994; Weiet al., 1994). Recently, an AAV vector has been approved for phase Ihuman trials for the treatment of cystic fibrosis.

AAV is a dependent parvovirus in that it requires coinfection withanother virus (either adenovirus or a member of the herpes virus family)to undergo a productive infection in cultured cells (Muzyczka, 1992). Inthe absence of coinfection with helper virus, the wild type AAV genomeintegrates through its ends into human chromosome 19 where it resides ina latent state as a provirus (Kotin et al., 1990; Samulski et al.,1991). rAAV, however, is not restricted to chromosome 19 for integrationunless the AAV Rep protein is also expressed (Shelling and Smith, 1994).When a cell carrying an AAV provirus is superinfected with a helpervirus, the AAV genome is “rescued” from the chromosome or from arecombinant plasmid, and a normal productive infection is established(Samulski et al., 1989; McLaughlin et al., 1988; Kotin et al., 1990;Muzyczka, 1992).

Typically, recombinant AAV (rAAV) virus is made by cotransfecting aplasmid containing the gene of interest flanked by the two AAV terminalrepeats (McLaughlin et al., 1988; Samulski et al., 1989; eachincorporated herein by reference) and an expression plasmid containingthe wild type AAV coding sequences without the terminal repeats, forexample pIM45 (McCarty et al., 1991; incorporated herein by reference).The cells are also infected or transfected with adenovirus or plasmidscarrying the adenovirus genes required for AAV helper function. rAAVvirus stocks made in such fashion are contaminated with adenovirus whichmust be physically separated from the rAAV particles (for example, bycesium chloride density centrifugation). Alternatively, adenovirusvectors containing the AAV coding regions or cell lines containing theAAV coding regions and some or all of the adenovirus helper genes couldbe used (Yang et al., 1994; Clark et al., 1995). Cell lines carrying therAAV DNA as an integrated provirus can also be used (Flotte et al.,1995).

c. Retroviral Vectors

Retroviruses have promise as gene delivery vectors due to their abilityto integrate their genes into the host genome, transferring a largeamount of foreign genetic material, infecting a broad spectrum ofspecies and cell types and of being packaged in special cell-lines(Miller, 1992).

The retroviruses are a group of single-stranded RNA virusescharacterized by an ability to convert their RNA to double-stranded DNAin infected cells by a process of reverse-transcription (Coffin, 1990).The resulting DNA then stably integrates into cellular chromosomes as aprovirus and directs synthesis of viral proteins. The integrationresults in the retention of the viral gene sequences in the recipientcell and its descendants. The retroviral genome contains three genes,gag, pol, and env that code for capsid proteins, polymerase enzyme, andenvelope components, respectively. A sequence found upstream from thegag gene contains a signal for packaging of the genome into virions. Twolong terminal repeat (LTR) sequences are present at the 5′ and 3′ endsof the viral genome. These contain strong promoter and enhancersequences and are also required for integration in the host cell genome(Coffin, 1990).

In order to construct a retroviral vector, a nucleic acid encoding agene of interest is inserted into the viral genome in the place ofcertain viral sequences to produce a virus that isreplication-defective. In order to produce virions, a packaging cellline containing the gag, pol, and env genes but without the LTR andpackaging components is constructed (Mann et al., 1983). When arecombinant plasmid containing a cDNA, together with the retroviral LTRand packaging sequences is introduced into this cell line (by calciumphosphate precipitation for example), the packaging sequence allows theRNA transcript of the recombinant plasmid to be packaged into viralparticles, which are then secreted into the culture media (Nicolas andRubenstein, 1988; Temin, 1986; Mann et al., 1983). The media containingthe recombinant retroviruses is then collected, optionally concentrated,and used for gene transfer. Retroviral vectors are able to infect abroad variety of cell types. However, integration and stable expressionrequire the division of host cells (Paskind et al., 1975).

Concern with the use of defective retrovirus vectors is the potentialappearance of wild-type replication-competent virus in the packagingcells. This can result from recombination events in which the intactsequence from the recombinant virus inserts upstream from the gag, pol,env sequence integrated in the host cell genome. However, new packagingcell lines are now available that should greatly decrease the likelihoodof recombination (Markowitz et al., 1988; Hersdorffer et al., 1990).

Gene delivery using second generation retroviral vectors has beenreported. Kasahara et al. (1994) prepared an engineered variant of theMoloney murine leukemia virus, that normally infects only mouse cells,and modified an envelope protein so that the virus specifically boundto, and infected, human cells bearing the erythropoietin (EPO) receptor.This was achieved by inserting a portion of the EPO sequence into anenvelope protein to create a chimeric protein with a new bindingspecificity.

d. Other Viral Vectors

Other viral vectors may be employed as expression constructs in thepresent invention. Vectors derived from viruses such as vaccinia virus(Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al., 1988),sindbis virus, cytomegalovirus and herpes simplex virus may be employed.They offer several attractive features for various mammalian cells(Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar etal., 1988; Horwich et al., 1990).

With the recent recognition of defective hepatitis B viruses, newinsight was gained into the structure-function relationship of differentviral sequences. In vitro studies showed that the virus could retain theability for helper-dependent packaging and reverse transcription despitethe deletion of up to 80% of its genome (Horwich et al., 1990). Thissuggested that large portions of the genome could be replaced withforeign genetic material. Chang et al. recently introduced thechloramphenicol acetyltransferase (CAT) gene into duck hepatitis B virusgenome in the place of the polymerase, surface, and pre-surface codingsequences. It was cotransfected with wild-type virus into an avianhepatoma cell line. Culture media containing high titers of therecombinant virus were used to infect primary duckling hepatocytes.Stable CAT gene expression was detected for at least 24 days aftertransfection (Chang et al., 1991).

In certain further embodiments, the vector will be HSV. A factor thatmakes HSV an attractive vector is the size and organization of thegenome. Because HSV is large, incorporation of multiple genes orexpression cassettes is less problematic than in other smaller viralsystems. In addition, the availability of different viral controlsequences with varying performance (temporal, strength, etc.) makes itpossible to control expression to a greater extent than in othersystems. It also is an advantage that the virus has relatively fewspliced messages, further easing genetic manipulations. HSV also isrelatively easy to manipulate and can be grown to high titers. Thus,delivery is less of a problem, both in terms of volumes needed to attainsufficient MOI and in a lessened need for repeat dosings.

e. Modified Viruses

In still further embodiments of the present invention, the nucleic acidsto be delivered are housed within an infective virus that has beenengineered to express a specific binding ligand. The virus particle willthus bind specifically to the cognate receptors of the target cell anddeliver the contents to the cell. A novel approach designed to allowspecific targeting of retrovirus vectors was recently developed based onthe chemical modification of a retrovirus by the chemical addition oflactose residues to the viral envelope. This modification can permit thespecific infection of hepatocytes via sialoglycoprotein receptors.

Another approach to targeting of recombinant retroviruses was designedin which biotinylated antibodies against a retroviral envelope proteinand against a specific cell receptor were used. The antibodies werecoupled via the biotin components by using streptavidin (Roux et al.,1989). Using antibodies against major histocompatibility complex class Iand class II antigens, they demonstrated the infection of a variety ofhuman cells that bore those surface antigens with an ecotropic virus invitro (Roux et al., 1989).

2. Other Methods of DNA Delivery

In various embodiments of the invention, DNA is delivered to a cell asan expression construct. In order to effect expression of a geneconstruct, the expression construct must be delivered into a cell. Asdescribed herein, the preferred mechanism for delivery is via viralinfection, where the expression construct is encapsidated in aninfectious viral particle. However, several non-viral methods for thetransfer of expression constructs into cells also are contemplated bythe present invention. In one embodiment of the present invention, theexpression construct may consist only of naked recombinant DNA orplasmids. Transfer of the construct may be performed by any of themethods mentioned which physically or chemically permeabilize the cellmembrane. Some of these techniques may be successfully adapted for invivo or ex vivo use, as discussed below.

a. Liposome-Mediated Transfection

In a further embodiment of the invention, the expression construct maybe entrapped in a liposome. Liposomes are vesicular structurescharacterized by a phospholipid bilayer membrane and an inner aqueousmedium. Multilamellar liposomes have multiple lipid layers separated byaqueous medium. They form spontaneously when phospholipids are suspendedin an excess of aqueous solution. The lipid components undergoself-rearrangement before the formation of closed structures and entrapwater and dissolved solutes between the lipid bilayers (Ghosh andBachhawat, 1991). Also contemplated is an expression construct complexedwith Lipofectamine (Gibco BRL).

Liposome-mediated nucleic acid delivery and expression of foreign DNA invitro has been very successful (Nicolau and Sene, 1982; Fraley et al.,1979; Nicolau et al., 1987). Wong et al. (1980) demonstrated thefeasibility of liposome-mediated delivery and expression of foreign DNAin cultured chick embryo, HeLa and hepatoma cells.

In certain embodiments of the invention, the liposome may be complexedwith a hemagglutinating virus (HVJ). This has been shown to facilitatefusion with the cell membrane and promote cell entry ofliposome-encapsulated DNA (Kaneda et al., 1989). In other embodiments,the liposome may be complexed or employed in conjunction with nuclearnon-histone chromosomal proteins (HMG-1) (Kato et al, 1991). In yetfurther embodiments, the liposome may be complexed or employed inconjunction with both HVJ and HMG-1. In other embodiments, the deliveryvehicle may comprise a ligand and a liposome. Where a bacterial promoteris employed in the DNA construct, it also will be desirable to includewithin the liposome an appropriate bacterial polymerase.

b. Electroporation

In certain embodiments of the present invention, the expressionconstruct is introduced into the cell via electroporation.Electroporation involves the exposure of a suspension of cells and DNAto a high-voltage electric discharge.

Transfection of eukaryotic cells using electroporation has been quitesuccessful. Mouse pre-B lymphocytes have been transfected with humankappa-immunoglobulin genes (Potter et al., 1984), and rat hepatocyteshave been transfected with the chloramphenicol acetyltransferase gene(Tur-Kaspa et al., 1986) in this manner.

c. Calcium Phosphate or DEAE-Dextran

In other embodiments of the present invention, the expression constructis introduced to the cells using calcium phosphate precipitation. HumanKB cells have been transfected with adenovirus 5 DNA (Graham and Van DerEb, 1973) using this technique. Also in this manner, mouse L(A9), mouseC127, CHO, CV-1, BHK, NIH3T3 and HeLa cells were transfected with aneomycin marker gene (Chen and Okayama, 1987), and rat hepatocytes weretransfected with a variety of marker genes (Rippe et al., 1990).

In another embodiment, the expression construct is delivered into thecell using DEAE-dextran followed by polyethylene glycol. In this manner,reporter plasmids were introduced into mouse myeloma and erythroleukemiacells (Gopal, 1985).

d. Particle Bombardment

Another embodiment of the invention for transferring a naked DNAexpression construct into cells may involve particle bombardment. Thismethod depends on the ability to accelerate DNA-coated microprojectilesto a high velocity allowing them to pierce cell membranes and entercells without killing them (Klein et al., 1987). Several devices foraccelerating small particles have been developed. One such device relieson a high voltage discharge to generate an electrical current, which inturn provides the motive force (Yang et al., 1990). The microprojectilesused have consisted of biologically inert substances such as tungsten orgold beads.

e. Direct Microinjection or Sonication Loading

Further embodiments of the present invention include the introduction ofthe expression construct by direct microinjection or sonication loading.Direct microinjection has been used to introduce nucleic acid constructsinto Xenopus oocytes (Harland and Weintraub, 1985), and LTK⁻ fibroblastshave been transfected with the thymidine kinase gene by sonicationloading (Fechheimer et al., 1987).

f. Adenoviral Assisted Transfection

In certain embodiments of the present invention, the expressionconstruct is introduced into the cell using adenovirus assistedtransfection. Increased transfection efficiencies have been reported incell systems using adenovirus coupled systems (Kelleher and Vos, 1994;Cotten et al., 1992; Curiel, 1994).

g. Receptor Mediated Transfection

Still further expression constructs that may be employed to delivernucleic acid construct to target cells are receptor-mediated deliveryvehicles. These take advantage of the selective uptake of macromoleculesby receptor-mediated endocytosis that will be occurring in the targetcells. In view of the cell type-specific distribution of variousreceptors, this delivery method adds another degree of specificity tothe present invention. Specific delivery in the context of anothermammalian cell type is described by Wu and Wu (1993; incorporated hereinby reference).

Certain receptor-mediated gene targeting vehicles comprise a cellreceptor-specific ligand and a DNA-binding agent. Others comprise a cellreceptor-specific ligand to which the DNA construct to be delivered hasbeen operatively attached. Several ligands have been used forreceptor-mediated gene transfer (Wu and Wu, 1987; Wagner et al., 1990;Perales et al., 1994; Myers, EPO 0273085), which establishes theoperability of the technique. In certain aspects of the presentinvention, the ligand will be chosen to correspond to a receptorspecifically expressed on the EOE target cell population.

In other embodiments, the DNA delivery vehicle component of acell-specific gene targeting vehicle may comprise a specific bindingligand in combination with a liposome. The nucleic acids to be deliveredare housed within the liposome and the specific binding ligand isfunctionally incorporated into the liposome membrane. The liposome willthus specifically bind to the receptors of the target cell and deliverthe contents to the cell. Such systems have been shown to be functionalusing systems in which, for example, epidermal growth factor (EGF) isused in the receptor-mediated delivery of a nucleic acid to cells thatexhibit upregulation of the EGF receptor.

In still further embodiments, the DNA delivery vehicle component of thetargeted delivery vehicles may be a liposome itself, which willpreferably comprise one or more lipids or glycoproteins that directcell-specific binding. For example, Nicolau et al. (1987) employedlactosyl-ceramide, a galactose-terminal asialganglioside, incorporatedinto liposomes and observed an increase in the uptake of the insulingene by hepatocytes. It is contemplated that the tissue-specifictransforming constructs of the present invention can be specificallydelivered into the target cells in a similar manner.

h. Homologous Recombination

Homologous recombination (Koller and Smithies, 1992) allows the precisemodification of existing genes, overcomes the problems of positionaleffects and insertional inactivation, and allows the inactivation ofspecific genes, as well as the replacement of one gene for another.Methods for homologous recombination are described in U.S. Pat. No.5,614,396, incorporated herein in its entirety by reference.

Thus a preferred method for the delivery of transgenic constructsinvolves the use of homologous recombination. Homologous recombinationrelies, like antisense, on the tendency of nucleic acids to base pairwith complementary sequences. In this instance, the base pairing servesto facilitate the interaction of two separate nucleic acid molecules sothat strand breakage and repair can take place. In other words, the“homologous” aspect of the method relies on sequence homology to bringtwo complementary sequences into close proximity, while the“recombination” aspect provides for one complementary sequence toreplace the other by virtue of the breaking of certain bonds and theformation of others.

Put into practice, homologous recombination is used as follows. First, asite for integration is selected within the host cell. Sequenceshomologous to the integration site are then included in a geneticconstruct, flanking the selected gene to be integrated into the genome.Flanking, in this context, simply means that target homologous sequencesare located both upstream (5′) and downstream (3′) of the selected gene.These sequences should correspond to some sequences upstream anddownstream of the target gene. The construct is then introduced into thecell, thus permitting recombination between the cellular sequences andthe construct.

As a practical matter, the genetic construct will normally act as farmore than a vehicle to insert the gene into the genome. For example, itis important to be able to select for recombinants and, therefore, it iscommon to include within the construct a selectable marker gene. Thisgene permits selection of cells that have integrated the construct intotheir genomic DNA by conferring resistance to various biostatic andbiocidal drugs. In addition, this technique may be used to “knock-out”(delete) or interrupt a particular gene. Thus, another approach foraltering or mutating a gene involves the use of homologousrecombination, or “knock-out technology”. This is accomplished byincluding a mutated or vastly deleted form of the heterologous genebetween the flanking regions within the construct. The arrangement of aconstruct to effect homologous recombination might be as follows:

-   -   . . . vector•5′-flanking sequence•selected gene• selectable        marker gene•flanking sequence-3′•vector . . .

Thus, using this kind of construct, it is possible, in a singlerecombinatorial event, to (i) “knock out” an endogenous gene, (ii)provide a selectable marker for identifying such an event and (iii)introduce a transgene for expression.

Another refinement of the homologous recombination approach involves theuse of a “negative” selectable marker. One example is the use of thecytosine deaminase gene in a negative selection method as described inU.S. Pat. No. 5,624,830. The negative selection marker, unlike theselectable marker, causes death of cells which express the marker. Thus,it is used to identify undesirable recombination events. When seeking toselect homologous recombinants using a selectable marker, it isdifficult in the initial screening step to identify proper homologousrecombinants from recombinants generated from random, non-sequencespecific events. These recombinants also may contain the selectablemarker gene and may express the heterologous protein of interest, butwill, in all likelihood, not have the desired phenotype. By attaching anegative selectable marker to the construct, but outside of the flankingregions, one can select against many random recombination events thatwill incorporate the negative selectable marker. Homologousrecombination should not introduce the negative selectable marker, as itis outside of the flanking sequences.

3. Marker Genes

In certain aspects of the present invention, specific cells are taggedwith specific genetic markers to provide information about the fate ofthe tagged cells. Therefore, the present invention also providesrecombinant candidate screening and selection methods which are basedupon whole cell assays and which, preferably, employ a reporter genethat confers on its recombinant hosts a readily detectable phenotypethat emerges only under conditions where a general DNA promoterpositioned upstream of the reporter gene is functional. Generally,reporter genes encode a polypeptide (marker protein) not otherwiseproduced by the host cell which is detectable by analysis of the cellculture, e.g., by fluorometric, radioisotopic or spectrophotometricanalysis of the cell culture.

In other aspects of the present invention, a genetic marker is providedwhich is detectable by standard genetic analysis techniques, such as DNAamplification by PCR™ or hybridization using fluorometric, radioisotopicor spectrophotometric probes.

a. Screening

Exemplary enzymes include esterases, phosphatases, proteases (tissueplasminogen activator or urokinase) and other enzymes capable of beingdetected by their activity, as will be known to those skilled in theart. Contemplated for use in the present invention is green fluorescentprotein (GFP) as a marker for transgene expression (Chalfie et al.,1994). The use of GFP does not need exogenously added substrates, onlyirradiation by near UV or blue light, and thus has significant potentialfor use in monitoring gene expression in living cells.

Other particular examples are the enzyme chloramphenicolacetyltransferase (CAT) which may be employed with a radiolabelledsubstrate, firefly and bacterial luciferase, and the bacterial enzymesβ-galactosidase and β-glucuronidase. Other marker genes within thisclass are well known to those of skill in the art, and are suitable foruse in the present invention.

b. Selection

Another class of reporter genes which confer detectable characteristicson a host cell are those which encode polypeptides, generally enzymes,which render their transformants resistant against toxins. Examples ofthis class of reporter genes are the neo gene (Colberre-Garapin et al.,1981) which protects host cells against toxic levels of the antibioticG418, the gene conferring streptomycin resistance (U.S. Pat. No.4,430,434), the gene conferring hygromycin B resistance (Santerre etal., 1984; U.S. Pat. Nos. 4,727,028, 4,960,704 and 4,559,302), a geneencoding dihydrofolate reductase, which confers resistance tomethotrexate (Alt et al., 1978), the enzyme HPRT, along with many otherswell known in the art (Kaufman, 1990).

D. Culture System

For long-term, high-yield production of a recombinant protein,polypeptide or peptide, stable expression is preferred. For example,cell lines that stably express constructs encoding a protein,polypeptide or peptide may be engineered. Rather than using expressionvectors that contain viral origins of replication, host cells can betransformed with vectors controlled by appropriate expression controlelements (e.g., promoter, enhancer, sequences, transcriptionterminators, polyadenylation sites, etc.), and a selectable marker.Following the introduction of foreign DNA, engineered cells may beallowed to grow for 1-2 days in an enriched media, and then are switchedto a selective media. The selectable marker in the recombinant plasmidconfers resistance to the selection and allows cells to stably integratethe plasmid into their chromosomes and grow to form foci which in turncan be cloned and expanded into cell lines.

A number of selection systems may be used, including, but not limitedto, the herpes simplex virus thymidine kinase (tk), hypoxanthine-guaninephosphoribosyltransferase (hgprt) and adenine phosphoribosyltransferase(aprt) genes, in tk⁻, hgprt⁻ or aprt⁻ cells, respectively. Also,antimetabolite resistance can be used as the basis of selection fordihydrofolate reductase (dhfr), that confers resistance to methotrexate;gpt, that confers resistance to mycophenolic acid; neomycin (neo), thatconfers resistance to the aminoglycoside G-418; and hygromycin (hygro),that confers resistance to hygromycin.

Animal cells can be propagated in vitro in two modes: as non-anchoragedependent cells growing in suspension throughout the bulk of the cultureor as anchorage-dependent cells requiring attachment to a solidsubstrate for their propagation (i.e., a monolayer type of cell growth).

Non-anchorage dependent or suspension cultures from continuousestablished cell lines are the most widely used means of large scaleproduction of cells and cell products. However, suspension culturedcells have limitations, such as tumorigenic potential and lower proteinproduction than adherent cells.

Large scale suspension culture of mammalian cells in stirred tanks is acommon method for production of recombinant proteins. Two suspensionculture reactor designs are in wide use—the stirred reactor and theairlift reactor. The stirred design has successfully been used on an8000 liter capacity for the production of interferon. Cells are grown ina stainless steel tank with a height-to-diameter ratio of 1:1 to 3:1.The culture is usually mixed with one or more agitators, based on bladeddisks or marine propeller patterns. Agitator systems offering less shearforces than blades have been described. Agitation may be driven eitherdirectly or indirectly by magnetically coupled drives. Indirect drivesreduce the risk of microbial contamination through seals on stirrershafts.

The airlift reactor, also initially described for microbial fermentationand later adapted for mammalian culture, relies on a gas stream to bothmix and oxygenate the culture. The gas stream enters a riser section ofthe reactor and drives circulation. Gas disengages at the culturesurface, causing denser liquid free of gas bubbles to travel downward inthe downcomer section of the reactor. The main advantage of this designis the simplicity and lack of need for mechanical mixing. Typically, theheight-to-diameter ratio is 10:1. The airlift reactor scales uprelatively easily, has good mass transfer of gases and generatesrelatively low shear forces.

It is contemplated that the proteins, polypeptides or peptides of theinvention may be “overexpressed”, i.e., expressed in increased levelsrelative to its natural expression in cells. Such overexpression may beassessed by a variety of methods, including radio-labeling and/orprotein purification. However, simple and direct methods are preferred,for example, those involving SDS/PAGE and protein staining or westernblotting, followed by quantitative analyses, such as densitometricscanning of the resultant gel or blot. A specific increase in the levelof the recombinant protein or peptide in comparison to the level innatural cells is indicative of overexpression, as is a relativeabundance of the specific protein in relation to the other proteinsproduced by the host cell and, e.g., visible on a gel.

E. Complementation

The terms “structural complementation”, “complementation” or “alphacomplementation” as used herein certain embodiments refers to theability of at least one polypeptide comprising a protein fragment ordomain to alter the activity of at least a second polypeptide comprisinga protein fragment or domain. In certain embodiments, the at least onepolypeptide and the at least second polypeptide are derived from thesame precursor protein sequence. A non-limiting example of this is thecomplementation of β-lactosidase's activity that occurs when theα-fragment and the ω fragment of β-lactosidase interact to produce anactive β-lactosidase enzymatic complex.

Other complementing protein fragments are known in the art. Non-limitingexamples include the P. falciparum thymidylate synthase anddihydrofolate reductase domains (Shallom et al., 1999), and the alphaand beta subunits of the mitochondrial processing peptidase of differentspecies (Adamec et al., 1999), whose activity was detected by the usedof temperature sensitive mutant yeast strains.

Thus, it is contemplated that various peptide or polypeptide sequencesmay be used to produce fusion proteins with a target protein, so thatthe folding of the target protein into a soluble form can be detectedvia the change in activity of the complemented peptide or polypeptide.It is also contemplated that additional complementing fragments ofcommonly used or well known selectable or screenable markers may be madefor use in the present invention. Non-limiting examples of such markersinclude a target binding protein, such as ubiquitin; an enzyme, such asβ-galactosidase, cytochrome c, chymotrypsin inhibitor, Rnase,phosphoglycerate kinase, invertase, staphylococcal nuclease, thioredoxinC, lactose permease, amino acyl tRNA synthase, or dihydrofolatereductase; a protein inhibitor, a fluorophore or a chromophore, such asgreen fluorescent protein, blue fluorescent protein, yellow fluorescentprotein, luciferase or aquorin.

It is contemplated that one or more fragments of such markers may beproduced through recombinant technology that is well known to those ofskill in the art, to produce an complementation system for assayingprotein folding as described herein. In a non-limiting example, anucleic acid encoding a N-terminal sequence of about 250 amino acids orless of a marker protein may be operatively associated with a nucleicacid of a protein of interest to be folded into soluble form. Suchnucleic acids may be used to construct an expression vector as describedherein, and used to complement a cell that expresses the C-terminalterminal sequence of the marker protein. In an alternative non-limitingexample, a nucleic acid encoding a C-terminal sequence of about 250amino acids or less of a marker protein may be operatively associatedwith a nucleic acid of a protein of interest to be folded into solubleform. Such nucleic acids may be used to construct an expression vectoras described herein, and used to complement a cell that expresses theN-terminal terminal sequence of the marker protein. Of course, one ofskill in the art may design nucleic acids encoding marker gene fragmentsof various lenghts. In certain embodiments, the marker gene fragment mayencode a polypeptide or peptide of less than about 200, about 150, about100, about 99, about 98, about 97, about 96, about 95, about 94, about93, about 92, about 91, about 90, about 89, about 88, about 87, about86, about 85, about 84, about 83, about 82, about 81, about 80, about79, about 78, about 77, about 76, about 75, about 74, about 73, about72, about 71, about 70, about 69, about 68, about 67, about 66, about65, about 64, about 63, about 62, about 61, about 60, about 59, about58, about 57, about 56, about 55, about 54, about 53, about 52, about51, about 50, about 49, about 48, about 47, about 46, about 45, about44, about 43, about 42, about 41, about 40, about 39, about 38, about37, about 36, about 35, about 34, about 33, about 32, about 31, about30, about 29, about 28, about 27, about 26, about 25, about 24, about23, about 22, about 21, about 20, about 19, about 18, about 17, about16, about 15, about 14, about 13, about 12, about 11, about 10, about 9,about 8, about 7, about 6, about 5, to about 4 amino acids, which isoperatively associated with the nucleic acid encoding the protein thatis soluble when folded correctly.

F. Screening Assays

The present invention is directed to the use of an α-complementationsystem to screen for various aspects of protein fold and/or solubility.As discussed above, an important aspect of the invention is the use of afusion protein that contains sequences from the protein of interest aswell as a portion of a marker protein. The marker protein, in thecontext of the fusion, is incapable of exhibiting its detectablephenotype. However, when expressed in an environment that also includesthe complementing portion of the marker protein, “complementation” takesplace and a detectable event occurs, assuming that the protein isproperly folded and remains soluble. This assay provides manyadvantages, including fidelity, sensitivity, ease of handling, and readyadaptability.

1. Methods

There are three primary applications for the invention: screening ofproteins for suitability in recombinant polypeptide production,screening for mutants or domain boundaries with altered folding and/orsolubility profiles (e.g., diagnosis of disease), and screening fordrugs that modulate protein folding and/or solubility. In the firstembodiment, the method includes the steps of:

-   -   a) providing an expression construct comprising (i) a gene        encoding a fusion protein, said fusion protein comprising a        protein of interest fused to a first segment of a marker        protein, wherein said first segment does not affect the folding        or solubility of the protein of interest, or affects it only is        a systematic (i.e., predictable and repeatable) manner and (ii)        a promoter active in said host cell and operably linked to said        gene;    -   b) expressing said fusion protein in a host cell that also        expresses a second segment of said marker protein, wherein said        second segment is capable of structural complementation with        said first segment; and    -   c) determining structural complementation.        By comparing the degree of structural complementation in the        method with that seen with appropriate negative controls,        changes in folding and/or solubility of said protein can be        determined. By looking at particular cell types from patients        suspected of having particular disease states, this general        method of screening can be transformed into a specific        diagnostic method.

In another embodiment, a method of screening for folding and/orsolubility mutants is provided, and includes the steps of:

-   -   a) providing a gene encoding fusion protein comprising (i) a        protein of interest and (ii) a first segment of a marker        protein, wherein said first segment does not affect the folding        or solubility of the protein of interest, or affects it only is        a systematic (ie., predictable and repeatable) manner, wherein        said fusion protein is not properly folded and/or soluble when        expressed in said host cell;    -   b) mutagenizing that portion of the gene encoding said protein        of interest;    -   c) expressing said fusion protein in a host cell that expresses        a second segment of said marker protein, wherein said second        segment is capable of structural complementation with said first        segment; and    -   d) determining structural complementation.        Again, a relative change in structural complementation, as        compared to the structural complementation observed with the        unmutagenized fusion protein, indicates a change in proper        folding and/or solubility of said protein. An alternative        embodiment involves the mutation of a gene of interest prior to        its fusion with the marker protein segment.

Finally, a third assay involves screening for candidate modulatorsubstances that modulate protein folding and/or solubility, includingthe steps of:

-   -   a) providing an expression construct comprising (i) a gene        encoding fusion protein, said fusion protein comprising a        protein of interest fused to a first segment of a marker        protein, wherein said first segment does not affect the folding        or solubility of the protein of interest, or affects it only is        a systematic (i.e., predictable and repeatable) manner, and (ii)        a promoter active in said host cell and operably linked to said        gene;    -   b) expressing said fusion protein in a host cell that expresses        a second segment of said marker protein, wherein said second        segment is capable of structural complementation with said first        segment;    -   c) contacting the host cell with said candidate modulator        substance; and    -   d) determining structural complementation.        Again, a relative change in structural complementation, as        compared to the structural complementation observed in the        absence of said candidate modulator substance, indicates that        said candidate modulator substance is a modulator of protein        folding and/or solubility

2. Modulators

As used herein the term “candidate substance” refers to any moleculethat may potentially inhibit or enhance protein folding and/orsolubility. The candidate substance may be a protein or fragmentthereof, a small molecule, or even a nucleic acid molecule. Using leadcompounds to help develop improved compounds is know as “rational drugdesign” and includes not only comparisons with know inhibitors andactivators, bu t predictions relating to the structure of targetmolecules.

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides or target compounds. By creating suchanalogs, it is possible to fashion drugs, which are more active orstable than the natural molecules, which have different susceptibilityto alteration or which may affect the function of various othermolecules. In one approach, one would generate a three-dimensionalstructure for a target molecule, or a fragment thereof. This could beaccomplished by x-ray crystallography, computer modeling or by acombination of both approaches.

It also is possible to use antibodies to ascertain the structure of atarget compound activator or inhibitor. In principle, this approachyields a pharmacore upon which subsequent drug design can be based. Itis possible to bypass protein crystallography altogether by generatinganti-idiotypic antibodies to a functional, pharmacologically activeantibody. As a mirror image of a mirror image, the binding site ofanti-idiotype would be expected to be an analog of the original antigen.The anti-idiotype could then be used to identify and isolate peptidesfrom banks of chemically- or biologically-produced peptides. Selectedpeptides would then serve as the pharmacore. Anti-idiotypes may begenerated using the methods described herein for producing antibodies,using an antibody as the antigen.

On the other hand, one may simply acquire, from various commercialsources, small molecule libraries that are believed to meet the basiccriteria for useful drugs in an effort to “brute force” theidentification of useful compounds. Screening of such libraries,including combinatorially generated libraries (e.g., peptide libraries),is a rapid and efficient way to screen large number of related (andunrelated) compounds for activity. Combinatorial approaches also lendthemselves to rapid evolution of potential drugs by the creation ofsecond, third and fourth generation compounds modeled of active, butotherwise undesirable compounds.

Candidate compounds may include fragments or parts ofnaturally-occurring compounds, or may be found as active combinations ofknown compounds, which are otherwise inactive. It is proposed thatcompounds isolated from natural sources, such as animals, bacteria,fungi, plant sources, including leaves and bark, and marine samples maybe assayed as candidates for the presence of potentially usefulpharmaceutical agents. It will be understood that the pharmaceuticalagents to be screened could also be derived or synthesized from chemicalcompositions or man-made compounds. Thus, it is understood that thecandidate substance identified by the present invention may be peptide,polypeptide, polynucleotide, small molecule inhibitors or any othercompounds that may be designed through rational drug design startingfrom known inhibitors or stimulators.

Other suitable modulators include antisense molecules, ribozymes, andantibodies (including single chain antibodies), each of which would bespecific for the target molecule. Such compounds are described ingreater detail elsewhere in this document. For example, an antisensemolecule that bound to a translational or transcriptional start site, orsplice junctions, would be ideal candidate inhibitors.

In addition to the modulating compounds initially identified, theinventors also contemplate that other sterically similar compounds maybe formulated to mimic the key portions of the structure of themodulators. Such compounds, which may include peptidomimetics of peptidemodulators, may be used in the same manner as the initial modulators.

3. Assay Formats

A quick, inexpensive and easy assay to run is an in vitro assay. Variouscell lines can be utilized for such screening assays, including cellsspecifically engineered for this purpose, as discussed in detail above.Depending on the assay, culture may be required. The cell is examinedusing α-complementation as a readout. Alternatively, molecular analysismay be performed, for example, looking at protein expression, mRNAexpression (including differential display of whole cell or polyA RNA)and others.

In vivo assays involve the use of various animal models, includingtransgenic animals that have been engineered to express both the fusionprotein (target protein+first marker segment) and the complementingmolecule (second marker segment). Due to their size, ease of handling,and information on their physiology and genetic make-up, mice are apreferred embodiment, especially for transgenics. However, other animalsare suitable as well, including insects, nematodes, rats, rabbits,hamsters, guinea pigs, gerbils, woodchucks, cats, dogs, sheep, goats,pigs, cows, horses and monkeys (including chimps, gibbons and baboons).Assays for modulators may be conducted using an animal model derivedfrom any of these species.

In such assays, one or more candidate substances are administered to ananimal, and the ability of the candidate substance(s) to alter proteinfolding and/or solubility, as compared to a similar animal not treatedwith the candidate substance(s), identifies a modulator.

Treatment of these animals with candidate substances will involve theadministration of the compound, in an appropriate form, to the animal.Administration will be by any route that could be utilized for clinicalor non-clinical purposes, including but not limited to oral, nasal,buccal, or even topical. Alternatively, administration may be byintratracheal instillation, bronchial instillation, intradermal,subcutaneous, intramuscular, intraperitoneal or intravenous injection.Specifically contemplated routes are systemic intravenous injection,regional administration via blood or lymph supply, or directly to anaffected site.

Determining the effectiveness of a compound in vivo may involve avariety of different criteria. Also, measuring toxicity and doseresponse can be performed in animals in a more meaningful fashion thanin in vitro or in cyto assays.

4. High Throughput and Flow Cytometry

High throughput formats are of particular use in drug screening. Flowcytometry involves the separation of cells or other particles in aliquid sample based upon signals generated in the host cells. Generally,the purpose of flow cytometry is to analyze the separated particles forone or more characteristics thereof. The basis steps of flow cytometryinvolve the direction of a fluid sample through an apparatus such that aliquid stream passes through a sensing region. The particles should passone at a time by the sensor and are categorized base on size,refraction, light scattering, opacity, roughness, shape, fluorescence,etc.

Rapid quantitative analysis of cells proves useful in biomedicalresearch and medicine. Apparati permit quantitative multiparameteranalysis of cellular properties at rates of several thousand cells persecond. These instruments provide the ability to differentiate amongcell types. Data are often displayed in one-dimensional (histogram) ortwo-dimensional (contour plot, scatter plot) frequency distributions ofmeasured variables. The partitioning of multiparameter data filesinvolves consecutive use of the interactive one- or two-dimensionalgraphics programs.

Quantitative analysis of multiparameter flow cytometric data for rapidcell detection consists of two stages: cell class characterization andsample processing. In general, the process of cell classcharacterization partitions the cell feature into cells of interest andnot of interest. Then, in sample processing, each cell is classified inone of the two categories according to the region in which it falls.Analysis of the class of cells is very important, as high detectionperformance may be expected only if an appropriate characteristic of thecells is obtained.

Not only is cell analysis performed by flow cytometry, but so too issorting of cells. In U.S. Pat. No. 3,826,364 (incorporated byreference), an apparatus is disclosed which physically separatesparticles, such as functionally different cell types. In this machine, alaser provides illumination which is focused on the stream of particlesby a suitable lens or lens system so that there is highly localizedscatter from the particles therein. In addition, high intensity sourceillumination is directed onto the stream of particles for the excitationof fluorescent particles in the stream. Certain particles in the streammay be selectively charged and then separated by deflecting them intodesignated receptacles. A classic form of this separation is viafluorescent tagged antibodies, which are used to mark one or more celltypes for separation.

Other methods for flow cytometry can be found in U.S. Pat. Nos.4,284,412; 4,989,977; 4,498,766; 5,478,722; 4,857,451; 4,774,189;4,767,206; 4,714,682; 5,160,974; and 4,661,913, all of which areincorporated by reference.

G. EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Materials and Methods

Antibodies, Chemicals and Expression Vectors

Monoclonal mouse anti-HA and polyclonal sheep anti-MBP antibodies werepurchased from BabCO (Richmond, Calif.). Horseradishperoxidase-conjugated (HRP) secondary antibodies were from JacksonImmunOResearch Laboratories (West Grove, Pa.).Isopropyl-β-D-thiogalactopyranoside (IPTG) and5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) were fromBoehringer Mannheim (Indianapolis, Ind.).O-nitrophenyl-β-D-galactopyranoside (ONPG) was purchased from Sigma (St.Louis, Mo.). The expression vector pMAL-c2×, coding for an MBP-α fusion,was from New England Biolabs (Beverly, Mass.). A plasmid containing cDNAfor the LivF protein of M. jannaschii (MJ1267) was obtained from theAmerican Type Culture Collection. Plasmid pAPP770 containing cDNA forthe Alzheimer's precursor protein (APP) was the generous gift of Dr. J.Herz, Dept. Molecular Genetics, UT Southwestern, Dallas, Tex. PlasmidpTRx.parallel1 containing cDNA for thioredoxin was the generous gift ofDr. K. Gardner, Dept. Biochemistry, UT Southwestern, Dallas, Tex.Plasmid pGex-2t containing cDNA for glutathione S-transferase was fromAmersham/Pharmacia (Piscataway, N.J.).

Construction of α-Fusion Expression Vectors

Complementary DNA fragments coding for residues 404-644 (NBD1-B) and419-655 (NBD1-D) of CFTR were excised using Nde1 and Xho1 from pET28aexpression plasmids generated as previously described (Qu & Thomas,1996). Based upon homology to the recently published H is P NBD crystalstructure (Hung et al., 1998), these constructs are predicted to containthe entire first NBD of CFTR. The resulting fragments were ligated intoNdeI/Sal1-digested pMal-c2× in place of the maltose-binding protein(MBP), forming an in-frame fusion with the α-fragment (residues 7-58from full length β-galactosidase). Expression cassette PCR was used toassmble the other α-fusion constructs examined. The MJ1267 cDNA was alsosubcloned into the Nde1 and Sal1 sites of pMal-c2×. The resulting vectorcontained an in-frame stop codon between MJ1267 and the polylinker ofpMAL-c2× which was removed by site-directed mutagenesis completing theα-fusion construct. TRx, GST and Aβ (APP residues 1-42) were eachligated into Nde1/Sac1-digested pMal-c2×. The cloning strategy used toassemble the tandem Aβ/α-fusion construct, Aβ-rpt, was similar to thatdescribed elsewhere (Culvenor et al., 1998), and utilized an internalEcoRI site to generate an exact Aβ(1-42) repeat with no interveningsequence. All targets were subcloned in the pMal-c2× vector and,therefore, utilize the same promoter. In addition, the ABC transporterNBDs evaluated were also expressed in BL21 cells under the control ofthe T7 promoter of pET28a. In each case, fidelity of PCR™ products andconstructs was verified by restriction mapping and DNA sequencing.

To serve as a marker for some of the expressed proteins (MJ1267,CFTR-NBD1, TRx, GST and Aβ), an HA-tag sequence was introduced into theSal1 site of the pMal-c2× expression vector using two annealedcomplimentary oligonucleotides coding for the tag sequence and flankedby Sal1 linker sequences. Correct orientation of the resulting ligationproducts was confirmed by DNA sequencing.

Site-Directed Mutagenesis

Oligonucleotide-directed mutagenesis using the QuickChange mutagenesiskit (Stratagene, La Jolla, Calif.) was performed to generate the mutantMBP proteins in the expression vector pMal-c2×. The sequences of theantisense mutagenic primers used are as follows: G32D/I33P -5′-GATGCTCAACGGTGACTTTAGGATCGGTATCTTCTCGAATTTC-3′ G32D -5′-CAACGGTGACTTTAATATCGGTATCTTTCTCG-3′ 133P -5′-GGTGACTTTAGGTCCGGTATCTTTCTCG-3′Mutation incorporation was verified by DNA sequencing. Plasmid DNA waspurified using reagents supplied by Qiagen Inc.Expression of Fusion Proteins

Expression constructs were transformed into DH5α E. coli by standardmethods and colonies selected on LB-agar plates supplemented with 100μg/mL ampicillin (amp). From single colonies, 10 mL LB+amp cultures wereinoculated and allowed to grow overnight at 37° C. The following day,the overnight culture was diluted 1000-fold into a fresh 10 mL LB+ampculture and allowed to grow to mid log phase (OD₆₀₀˜0.5). Proteinproduction was induced by the addition of IPTG to 0.3 mM and the cellswere further incubated for the indicated times.

In Vitro Assay of β-gal Complementation

After the completion of fusion protein expression, cells (1.5 mL) wereharvested by centrifugation at 10,000×g for two minutes. After removalof the supernatants, the cell pellets were resuspended in 1 mL of bufferZ (10 mM KCl, 2.0 mM MgS04, 100 mM NaHP04, pH 7.0). The cells werepelleted again, resuspended in 0.3 mL buffer Z and lysed by threefreeze/thaw cycles between liquid nitrogen and a 37° C. water bath.Next, 0.1 mL of the resulting cell lysate was transferred to a cleanmicrofuge tube to which buffer Z (0.7 ml) supplemented with 0.27%β-mercaptoethanol was added. Reactions were initiated by the addition of160 μL of ONPG solution (4.0 mg/mL dissolved in buffer Z) and incubatedat 37° C. for 10 min. Reactions were quenched by the addition of 0.4 mL1 M Na₂CO₃. Tubes were then centrifuged at 10,000×g for 10 min to removedebris and the supernatant's absorption at 420 nm was measured.

Analysis of Soluble and Insoluble Fractions

To biochemically analyze the solubility characteristics of the expressedfusion proteins, 3 mL of culture from cells induced for the indicatedtimes was harvested by centrifugation, washed once and resuspended in600 μL lysis solution (100 mM NaCl, 1 mM EDTA, 50 mM Tris Cl, pH 7.6).The cell suspensions were lysed by sonication three times for 30 sec at50° C. duty cycle and power output of 4 using a Branson model 450sonifier fit with a microtip probe. All manipulations were carried outon ice. After sonication, the solution was centrifuged to separatesoluble and insoluble fractions at 10,000×g in a microfuge at 4° C. for10 min. Supernatant and pellet fractions were analyzed by SDS PAGE andWestern blotting where appropriate.

SDS PAGE and Western Blotting

Expressed proteins were analyzed by electrophoresis through 10%Tricine-SDS polyacrylamide gels using the buffer system of Schagger andvon Jagow (1987). Protein bands were visualized by staining withcoomassie blue. For Western immunoblotting, standard methods wereemployed for transfer of proteins from gels to nitrocellulose. Resultingmembranes were blocked in TBS containing Tween-20 and 10% dehydratedmilk for at least 1 hr and incubated at room temperature with theindicated primary antibodies. Immunoreactive bands were visualized byECL (Amersham, Piscataway, N.J.) using appropriate HRP-conjugatedsecondary antibodies and X-ray film. The density of bands on coomassiestained gels and exposed x-ray film were measured on an Agfa Arcusscanner and quantified using Molecular Analyst software (BioRad,Hercules, Calif.).

Blue/White Screening for β-gal Complementation

Single colonies of DH5α containing the individual expression constructswere analyzed for the ability of the α-fusion proteins to complementβ-gal activity in vivo. Bacteria harboring each construct were streakedto single colonies on LB-agar plates supplemented with 100 μg/mLampicillin, 80 μg/mL Xgal, and 0.1 mM IPTG. The plates were incubated at37° C. for 18 to 48 hr and activity of β-gal was assessed byvisualization of blue color in α-complementing colonies.

Colorimetric Screening for β-gal Complementation in 96-Well Plates

Cells harboring each of the indicated expression constructs were grownto mid log phase (OD₆₀₀˜0.5) from overnight cultures as described above.125 μl of each culture ws transferred to individual wells of aflat-bottom 96-well plate containing 125 μl LB media supplemented with100 μg/mL ampicillin and 0.6 mM IPTG (resulting in a final [IPTG] of 0.3mM). The plates were then placed on an orbit shaker at 37° C. with rapidshaking. After induction for 1 hr, X-gal was added to a finalconcentration of 80 μg/mL, and the plate was returned to the shaker at37° C. overnight.

Example 2 Results

In order to test the ability of α-fragment chimeras to complement theω-fragment of β-gal and report target protein solubility by productingactive β-gal, model polypeptides were fused to the N-terminus of theα-fragment in an inducible bacterial expression plasmid (FIG. 1B).Initial experiments focused on the maltose binding protein (MBP) of E.coli. MBP is normally secreted into the periplasm of E. coli, however,the construct used in the present study lacks the required leadersequence and therefore, folds in the cytoplasm where the ω-fragment islocated.

To assess the relative abilities of the expressed α-fusion proteins tocomplement β-gal activity in vivo, E. coli harboring the fusionexpression constructs were plated on IPTG/X-gal indicator plates and thedevelopment of blue color in resulting colonies was monitored.pUC19-transformed DH5α E. coli, which express a 54 residue α-fragment(residues 659 of β-gal), are the most intensely blue. This representsthe level of 1-gal complementation attributable to the α-fragment alone.The MBP-α fusion protein (MBP residues 1-366, a: residues 7-58 of 1-gal)also yields significant α-complementation, although less than observedfor pUC19. Yanisch-Perron et al. (1985).

Previously, several mutations were identified which lead to diminishedsolubility and reduced periplasmic yield of MBP (Betton Hofnung, 1986).For example, mutation of two residues, 133P and G32D, decreased solubleperiplasmic MBP by more than 100-fold. This double mutation wasintroduced into MBP/a fusion construct, and monitored forα-complemenation on indicator plates. The wild-type MPB and the doublemutant expressed at equivalent levels. Consistent with the previouslyreported effect of these mutations on the in vivo solubility of MBP; theG32D/I33P double mutation significantly impaired the solubility and,thus, ability of the fusion protein to complement β-gal activity onindicator plates.

To test the generality of the assay system, a series of α-fusionconstructs were generated. Fusion to a of either TRx or GST (two highlysoluble proteins used regularly as fusions to aid in the solubility ofill-behaved partners) and express in DH5α on indicator plates results inblue color development that is as intense as that observed for the MBP/afusion construct. Next, a series of nucleotide binding domains (NBD)from two ATP binding-cassette (ABC) transporters were generated andexamined. Two are polypeptides predicted to include the first NBD of thecystic fibrosis transmembrane conductance regulator (CFTR): NBD1-B (CFTRresidues 404-644), and NBD1-D (CFTR residues 419-655). This domain haspoor solubility properties due either to inherently limited solubilityin the absence of other domains of the protein with which it normallyinteracts, or to marginal stability/misfolding or both. Severalmutations within this domain prevent proper folding of the full lengthCFTR in vivo and, thus, lead to cystic fibrosis. The third NBD, LivF(MJ1267), is a subunit of the branched chain amino acid transporter fromthe hyperthermophilic archaeon M. jannaschi. CFTR NBD1 has been shown tobe insoluble, forming inclusion bodies when expressed in E. coli (Qu &Thomas, 1996), unless fused to soluble protein such as wild-type MBP (Koet al., 1993) or GST (King & Sorscher, 1998). MJ1267, however, hasproven much more soluble, yielding 10% soluble protein from a T7expression system in BL21 E. coli.

When expressed in DH5α on indicator plates, both CFTR NBD/α fusionsresult in very little blue color, even after 48 hr of growth, althoughthe NBD1-D/α fusion appears to complement measurably more than NBD1-B.By contrast, expression of the MJ1267/a fusion results in asignificantly elevated level of blue color when compared to either ofthe CFTR NBD/a fusion proteins. The MBP/a fusion proteins express athigher levels than the NBD/a fusions as a group, and thus more activity.It should be noted that relative levels of α-complementation, asevidenced by blue color on indicator plates, can be observed at thesingle colony level for each of the constructs tested, providing ameasure that is independent of plated cell density.

To test whether the α-complementation assay is adaptable to a formatamenable to rapid-throughput screening, the constructs described abovewere analyzed for the development of blue color in a 96-well plate β-galassay. The levels of blue color obtained in the micro titer plate assayfor each construct agrees well with that obtained in the agar plateassay. In fact, the difference in color levels observed upon comparisonof the two CFTR-NBD/α-fusions is more apparent in the 96-well plateassay.

To verify the hypothesis that the intensity of blue color on indicatorplates is reporting target protein solubility, the amount of solubleversus insoluble protein was measured in biochemical fractionationexperiments. E. coli expressing wild-type, G32D, 133P, andG32D/I33P-MBP/α fusions were subjected to cell disruption andfractionation by centrifugation. Analysis by SDS PAGE of the soluble andinsoluble fractions for each fusion protein revealed a correlationbetween solubility and level of blue color on Xgal plates. It isimportant to note that the aga plate β-gall assay, after long incubationtimes, is most sensitive to changes from insoluble to higher levels ofsolubility, the range of greatest practical utility. The wild-type MBP/αfusion fractionates primarily to the supernatant, while the doublemutant (G32D/I33P) fractionates primarily to the pellet. Fractionationresults were further confirmed by Western blots probed with anti-MBPantibodies. The fraction of MBP/a fusions that are soluble is inagreement with the previously published stability and folding yield ofthese mutants without the α-fragment marker (Betton & Hofnung, 1996).This suggests that the α-fragment does not significantly impact theoverall solubility characteristics of the MBP fusion proteins and istherefore a good reporter of target protein solubility. Similarly, thehigh levels of blue color observed for the GST/a and TRx/a fusionscorrelates well with the biochemical fractionation experiments, whichindicate a majority of both of these proteins partions to the solublefraction.

A correlation between the biochemical solubility and α-complementation(as indicated by blue color of colonies in the plate assays) also wasdemonstrated for the NBD/a fusion constructs. Both CFTR NBD/a fusionproteins exhibit little to no blue color, and virtually all of thefusion protein partitions to the insoluble fraction whether expressedwith (DH5α expression) or without (BL21 expression) the α-fragment. Incontrast, MJ1267, when expressed as an α-fragment fusion, produces asignificantly higher level of blue color relative to either of theCFTR-NBD/a fusions. This correlates with the partial solubility ofMJ1267 either with (DH5α expreression) or without (BL21 expression) theα-fragment. Taken together, these results suggest that in these cases,the relatively small α-fragment, when fused to a target polypeptide,does not have large effects on the target's solubility; neitherincreasing that of the otherwise insoluble targets (CFTR-NBDs), nordecreasing that of the partially soluble one (MJ1267).

A quantitative measure of α-complementation of β-gal by each of thefusion targets was obtained by the direct measurement of activity incell lysates. A total of four MBP folding variants were utilized toestablish the quantitative relationship within a target system between1-gal activity and biochemical solubility. Table 3 summarizes theresults of these in vitro enzyme assays. TABLE 3 Target Protein β-galActivity (units/cell) MBP wild-type 102 +/− 19 G32D  94 +/− 21 I33P  46+/− 12 G32D/I33P  14 +/− 3 GST 134 +/− 8 TRx 159 +/− 14 CFTR NBD1-B  5+/− 1 CFTR NBD1-D  6 +/− 2 MJ1267 (LivF)  12 +/− 6A unit of β-gall activity is defined as the amount of enzyme required tohydrolyze one μmole of ONPG to o-nitrophenol and D-galactose per minute.Note that the polylinker between MBP (and mutants thereof) and theα-fragment is 36 residues in length. This linker was reduced to 9residues during construction of the CFTR-, LivF-, GST-, and TRx-α fusionconstructs.Activity correlates well with the relative levels of blue color observedfor these constructs. The plate assay is less able to distinguish highlysoluble targets from those of intermediate solubility (MBP singlemutants) most likely due to integration of the signal during growth ofthe colonies. FIG. 2 shows a linear relationship between the enzymaticactivity (Table 3) and the biochemical soluble fraction for each of theMBP/α fusions as assessed by densitometry of Coomassie-stained gels.Again, the activities show a linear correlation with the periplasmicfolding yields for the unfused MBPs reported by Betton and Hofnung(1996), further supporting the assay's ability to report on theintrinsic folding/solubility properties of the target proteins. Thediffering magnitude of the effects reported here when compared withthose previously reported by Betton and Hofnung (1996) may reflect thecellular environments where folding takes place since the presentconstructs must fold in the cytoplasm.

In addition to cystic fibrosis, many other human diseases are associatedwith inappropriate folding and/or aggregation of proteins (Thomas etal., 1995; Tan & Pepys, 1994; Wells & Warren, 1998). To test whether thestructural complementation assay has application to such proteins, theAlzheimer's Aβ (1-42) peptide, which forms insoluble fibrils in thebrains of affected individuals, was selected as an additional test case.When fused to the α-fragment and expressed in E. coli on indicatorplates, the fusion protein is unable to efficiently complement β-galactivity, resulting in very little development of blue color. Incontrast, mutation of phenylalanine to proline at position 19 of Aβ(F19P), a mutation known to retard fibril formation in vitro (Wood etal., 1995), results in a clear and measurable increase in blue color onindicator plates, approximately a three-fold increase in β-gal activity,and increased fusion protein in the soluble fraction at equivalentlevels of expression. Recently, Culvenor and co-workers reported theproduction of “large intracellular deposits” of Aβ-immunoreactivematerial upon the expression of Aβ(1-42) as a tandem head-to-tail duplexin yeast (Culvenor et al., 1998). To assess the ability of this assay toreport on the solubility state of such a construct, the inventorsassembled and expressed a tandem repeat of Aβ as a fusion with theα-fragment (Aβ-rpt). Colonies expressing the Aβ-rpt/a fusion proteinexhibit no detectable blue color on indicator plates, in vitro β-galactivity less than that observed for the wild-type Ap/a fusion, and nodetectable protein is in the soluble fraction. Interestingly, the AP-rptprotein aggregates to form a ladder of increasingly higher molecularweight insoluble species, a property absent from the single Ap/a fusionand perhaps more reflective of the disease condition.

All of the compositions and/or methods disclosed and claimed herein canbe made and executed without undue experimentation in light of thepresent disclosure. While the compositions and methods of this inventionhave been described in terms of preferred embodiments, it will beapparent to those of skill in the art that variations may be applied tothe compositions and/or methods and in the steps or in the sequence ofsteps of the method described herein without departing from the concept,spirit and scope of the invention. More specifically, it will beapparent that certain agents which are both chemically andphysiologically related may be substituted for the agents describedherein while the same or similar results would be achieved. All suchsimilar substitutes and modifications apparent to those skilled in theart are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

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1-29. (canceled)
 30. a method of screening for protein stability,folding and/or solubility mutants comprising: a) providing a geneencoding a fusion protein comprising (i) a protein of interest and (ii)a first segment of a marker protein, wherein said first segment does notaffect the folding or solubility of the protein of interest, whereinsaid fusion protein is unstable, not properly folded and/or not solublewhen expressed in said host cell; b) mutagenizing that portion of thegene encoding said protein of interest; c) expressing said fusionprotein in a host cell that expresses a second segment of said markerprotein, wherein said second segment is capable of structuralcomplementation with said first segment; and d) determining structuralcomplementation, wherein a relative increase in structuralcomplementation, as compared to the structural complementation observedwith the unmutagenized fusion protein, indicates an increase instability, proper folding and/or solubility of said protein.
 31. Themethod of claim 30, wherein said fusion is C-terminal to said protein ofinterest.
 32. The method of claim 30, wherein said fusion is N-terminalto said protein of interest.
 33. The method of claim 30, wherein saidmarker protein is selected from the group consisting of a target bindingprotein, an enzyme, a protein inhibitor, a chromophore.
 34. The methodof claim 30, wherein said host cell is selected from the groupconsisting of a bacterial cell, an insect cell, a yeast cell, a nematodecell, a mammalian cell. 35-40. (Canceled)
 41. The method of claim 30,wherein the unmutagenized fusion protein is unstable.
 42. The method ofclaim 30, wherein the unmutagenized fusion protein is not properlyfolded.
 43. The method of claim 30, wherein the unmutagenized fusionprotein is not soluble.